Lecture 2

Question 1

The cytoplasm is comprised of what two main things
Where is the cytoplasm located?

1. Where is the cytoplasm located in eukaryotic cells?
   • A. Inside the nucleus
   • B. Enclosed within the cell membrane and surrounding the nucleus
   • C. Only in the cell membrane
   • D. In the mitochondria
   2. Which of the following is NOT typically found in the cytoplasm?
      • A. Organelles
      • B. Inclusions
      • C. Nucleus
      • D. Cytosol
   3. The cytoplasm of a cell is composed of which of the following?
      • A. Only organelles
      • B. Only inclusions
      • C. Inclusions and organelles
      • D. The cell membrane and nucleus
2. Which of the following structures is typically found suspended in the cytoplasm?
   • A. Mitochondria
   • B. Nucleus
   • C. Nucleolus
   • D. Nuclear envelope
   5. What is the primary function of inclusions in the cytoplasm?
      • A. To carry out cellular respiration
      • B. To store various substances like nutrients, pigments, and waste products
      • C. To synthesize proteins
      • D. To maintain the structural integrity of the cell

Which of the following statements is true about the cytosol?
• A. It is a membrane-bound organelle
• B. It is the gel-like substance in which organelles are suspended
• C. It is responsible for packaging proteins
• D. It is the primary site of cellular respiration

Answer 1

Localization:
- Position: The cytoplasm is a gel-like substance enclosed within the cell membrane (plasma membrane) and surrounds the cell nucleus in eukaryotic cells. It fills the space between the cell membrane and the nucleus.

Comprised of:
Inclusions
Organelles

1. Where is the cytoplasm located in eukaryotic cells?
   • A. Inside the nucleus
   • B. Enclosed within the cell membrane and surrounding the nucleus
   • C. Only in the cell membrane
   • D. In the mitochondria
   Answer: B. Enclosed within the cell membrane and surrounding the nucleus
   
   2. Which of the following is NOT typically found in the cytoplasm?
      • A. Organelles
      • B. Inclusions
      • C. Nucleus
      • D. Cytosol
      Answer: C. Nucleus

In MCQ 2, the question asks which of the listed options is NOT typically found in the cytoplasm.

• A. Organelles: Organelles, such as mitochondria, endoplasmic reticulum, and Golgi apparatus, are embedded within the cytoplasm. They are integral components of the cytoplasm.
• B. Inclusions: Inclusions, such as pigment granules, lipid droplets, or glycogen granules, are also present in the cytoplasm and serve various functions depending on the cell type.
• C. Nucleus: The nucleus is not located in the cytoplasm. It is enclosed by the nuclear envelope and resides in its own space within the cell, separate from the cytoplasm.
• D. Cytosol: The cytosol is the liquid component of the cytoplasm in which organelles and inclusions are suspended.

Explanation for the Correct Answer (C):
The nucleus is a distinct structure within the cell, separated from the cytoplasm by the nuclear envelope. It is not part of the cytoplasm but rather a separate compartment within the cell. The cytoplasm consists of the cytosol and the structures (organelles and inclusions) suspended within it.

3.	The cytoplasm of a cell is composed of which of the following?
•	A. Only organelles
•	B. Only inclusions
•	C. Inclusions and organelles
•	D. The cell membrane and nucleus Answer: C. Inclusions and organelles

4. Which of the following structures is typically found suspended in the cytoplasm?
   • A. Mitochondria
   • B. Nucleus
   • C. Nucleolus
   • D. Nuclear envelope
   Answer: A. Mitochondria
   
   5. What is the primary function of inclusions in the cytoplasm?
      • A. To carry out cellular respiration
      • B. To store various substances like nutrients, pigments, and waste products
      • C. To synthesize proteins
      • D. To maintain the structural integrity of the cell
      Answer: B. To store various substances like nutrients, pigments, and waste products

Which of the following statements is true about the cytosol?
• A. It is a membrane-bound organelle
• B. It is the gel-like substance in which organelles are suspended
• C. It is responsible for packaging proteins
• D. It is the primary site of cellular respiration
Answer: B. It is the gel-like substance in which organelles are suspended

Question 2

What are inclusions
Inclusions are living cytoplasmic materials true or false
Are inclusions membrane bound or enclosed in a membrane ?
Under the microscope in a lab, it showed lots of lipid droplets as inclusions in the cytoplasm. Which tissues or organs will these kind of cells with this kind of inclusions majorly be found in?
What if it had showed plenty glycogen granules as inclusions. Which tissues or organs will these kind of cells with this kind of inclusions majorly be found in?
What if it had showed plenty pigments as inclusions. Which tissues or organs will these kind of cells with this kind of inclusions majorly be found in?

Answer 2

Non-living cytoplasmic materials. They are various types of particles or substances that are present within the cell but are not enclosed by a membrane
They are usually not surrounded by a plasma membrane

Eg. lipids, glycogen, pigment granules.

Inclusions:
- Glycogen Granules: In some cells, particularly in liver and muscle cells, glycogen granules (storage form of glucose) can be found in the cytoplasm.
- Lipid Droplets: Adipocytes and certain other cells store lipids as lipid droplets in the cytoplasm.
- Pigments: Some cells contain pigments, such as melanin in melanocytes, stored in the cytoplasm.
- Storage Granules: Cells may store various substances in the cytoplasmic matrix as storage granules, depending on their specific function.

Question 3

What are organelles?
State the two main types of the organelles and give examples under each type
What is the difference between a centromere,a centriole,a centrosome and a micro tubule

Answer 3

Organelles are the organ systems of the cell.
Little ‘organs’
A specialised subunit within a cell that has a specific function

Types:
- Membraneous (membrane-limited compartments)
- Non-membraneous. Eg. Microtubules.

Organelles within cells can be categorized into membranous and non-membranous types, each serving distinct functions and roles in cellular physiology:

1. Nucleus:
   
   • Contains genetic material (DNA) and regulates gene expression.
   • Surrounded by a double membrane (nuclear envelope) with pores for molecular transport.
2. Endoplasmic Reticulum (ER):
   
   • Rough ER: Studded with ribosomes; involved in protein synthesis, folding, and transport.
   • Smooth ER: Involved in lipid synthesis, detoxification, and calcium storage.
3. Golgi Apparatus:
   
   • Modifies, sorts, and packages proteins and lipids from the ER for transport to other parts of the cell or for secretion.
4. Mitochondria:
   
   • Powerhouse of the cell; site of aerobic respiration and ATP production.
   • Double membrane structure with inner folds (cristae) for increased surface area.
5. Lysosomes:
   
   • Contain digestive enzymes for breaking down macromolecules, old organelles, and pathogens.
   • Formed from the Golgi apparatus and have a single membrane.
6. Vacuoles (in plant cells):
   
   • Large membrane-bound sacs involved in storage of water, ions, sugars, and pigments.
   • Help maintain turgor pressure and support structure in plant cells.

1. Ribosomes:
   
   • Site of protein synthesis; can be free in the cytoplasm or attached to the rough ER.
   • Composed of RNA and protein but not enclosed by a membrane.
2. Cytoskeleton:
   
   • Network of protein filaments that provide structure, support, and facilitate movement within the cell.
   • Includes microfilaments (actin), intermediate filaments, and microtubules (hollow tubes made of tubulin).
3. Centrioles:
   
   • Paired structures involved in organizing microtubules during cell division (mitosis and meiosis).
   • Found in animal cells and some lower plants. Have three by 9 something something. When you look at the picture, you’ll understand.
     • Centrioles are present in animal cells, but not plant cells
     • Centrioles are used for animal cells to reproduce.
     They release long, stiff fibers called microtubules that split the cell apart during cell division.
     centrioles are organelles which are only active during cell division.
     They produce spindle fibers which attach to chromosomes. The fibers pull a copy of each chromosome to opposite sides of the cell so that
     when it splits , each new daughter cell has all the DNA It needs
4. Centrosomes:
   
   • Region near the nucleus that contains centrioles and regulates cell cycle progression and organization of the cytoskeleton.
5. Microtubules:
   
   • Hollow tubes made of tubulin protein; part of the cytoskeleton involved in cellular movement, transport, and structural support.

So centrosomes contain two centrioles and those centrioles contain microtubules
Centromere holds two sister chromatids together in a replicated chromosome.
Look a picture to see how it all comes together

Question 4

State two functions of the nucleus
What is the nuclear envelope,nucleoplasm
Where are Lamins found? And what are their functions
What in the nucleus is responsible for chromatin
organization,regulation of replication and transcription

Answer 4

Contain DNA in the form of chromatin (genetic material). Functions in transmission and expression of genetic material.

Genetic information for RNA and protein synthesis is encoded in the DNA

Nucleus is surrounded by nuclear envelope(envelope is made up of inner and outer parts). There are pores in the envelope that are responsible for the transport of materials from nucleus into the cytoplasm and vice versa.

Inner and outer membranes of nucleus

The nucleus, a membrane-bound organelle within eukaryotic cells, consists of two distinct membranes that define its structure and function:

1. Structure: The inner membrane of the nucleus, also known as the nuclear lamina, is a dense network of proteins that lines the inner surface of the nuclear envelope.
2. Function:
   
   • Support and Structure: Provides structural support to the nucleus and helps maintain its shape.
   • Attachment Site: Anchors chromatin (DNA and associated proteins) and nuclear pores, facilitating communication between the nucleus and cytoplasm.
   • Regulation: Plays a role in gene regulation and chromatin organization.

1. Structure: The outer membrane of the nucleus is a double membrane structure that surrounds the nucleus, forming the nuclear envelope.
2. Function:
   
   • Barrier: Acts as a selective barrier between the nucleoplasm (inside the nucleus) and the cytoplasm (outside the nucleus), controlling the movement of molecules in and out of the nucleus.
   • Nuclear Pores: Contains nuclear pores that regulate the transport of proteins, RNA, and other molecules between the nucleus and cytoplasm.
   • Integration with Endoplasmic Reticulum (ER): In certain cell types, the outer nuclear membrane is continuous with the rough endoplasmic reticulum (ER), facilitating the exchange of membrane components and maintaining cellular integrity.

• Composition: The nuclear envelope consists of the outer and inner nuclear membranes, nuclear pores, and the space between the membranes called the perinuclear space.

Yes, you’re correct. The nucleus in eukaryotic cells is indeed surrounded by a double membrane structure known as the nuclear envelope. Here’s a clearer breakdown:

1. Structure:
   
   • Outer Membrane: A double-layered membrane that is continuous with the endoplasmic reticulum (ER) in certain regions of the cell. It is studded with ribosomes and involved in protein synthesis and membrane production.
   • Inner Membrane: A lipid bilayer that is lined with proteins and supports the nuclear envelope’s shape and structure.lamins are found here. Lamins and the nuclear lamina are crucial for maintaining nuclear integrity, regulating gene expression, and ensuring proper nuclear function in eukaryotic cells.Lamins are responsible for chromatin organization,regulation of replication and transcription
     Lamins form a scaffold for structure called nuclear lamina
2. Function:
   
   • Barrier: The nuclear envelope separates the contents of the nucleus (genetic material and nucleoplasm) from the cytoplasm of the cell, providing compartmentalization and protection.
   • Regulation: Nuclear pores embedded in the nuclear envelope regulate the passage of molecules such as RNA, proteins, and ions between the nucleus and cytoplasm, controlling cellular activities and gene expression.
   • Integration with Endoplasmic Reticulum (ER): The outer membrane of the nuclear envelope is continuous with the rough ER, facilitating the exchange of membrane components and ensuring coordination between nuclear and cellular functions.

• Location: The nucleus is centrally located within the cell, surrounded by the nuclear envelope.
• Content: It contains the genetic material (DNA), which is organized into chromosomes and associated proteins called chromatin. The nucleoplasm is the fluid inside the nucleus where chromatin, nucleolus(Location: It is located within the nucleus, typically appearing as a dense, spherical region not surrounded by a membrane.
  
  2. Composition: The nucleolus is primarily composed of RNA (ribosomal RNA or rRNA) and proteins. It lacks a membrane and is instead organized by the genetic material it synthesizes.), and other nuclear components are suspended.

The nucleus, enclosed within the nuclear envelope, is a crucial organelle responsible for housing genetic material and coordinating cellular activities through the regulation of gene expression and molecular transport. The nuclear envelope serves as a protective barrier while enabling communication and integration between the nucleus and the rest of the cell, essential for maintaining cellular functions and integrity.

Question 5

What disease does mutation in Lamins cause

Answer 5

. These disorders are typically characterized by abnormalities in tissues where lamins are highly expressed, such as muscle, adipose tissue, and the nervous system.

1. Emery-Dreifuss Muscular Dystrophy (EDMD): This is a genetic muscle disorder characterized by muscle wasting and weakness, joint stiffness, and cardiac conduction abnormalities. Mutations in the LMNA gene, which encodes lamins A and C, are associated with EDMD.
2. Hutchinson-Gilford Progeria Syndrome (HGPS): HGPS is a rare genetic disorder that causes rapid aging in children. It is caused by a specific mutation in the LMNA gene, resulting in the production of an abnormal form of lamin A called progerin. Progerin disrupts nuclear structure and function, leading to premature aging symptoms.child ages very fast.
3. Dilated Cardiomyopathy with Conduction System Disease: Mutations in the LMNA gene can also cause dilated cardiomyopathy, a condition where the heart muscle becomes weakened and enlarged, affecting its ability to pump blood efficiently. This condition is often associated with conduction system abnormalities that can lead to arrhythmias.
4. Charcot-Marie-Tooth Disease (CMT) Type 2B1: CMT is a group of inherited neurological disorders affecting the peripheral nerves. Type 2B1 is caused by mutations in the LMNA gene, leading to peripheral nerve dysfunction and muscle weakness.
5. Restrictive Dermopathy: This is a severe skin disorder characterized by tight, rigid skin that restricts movement. It is caused by mutations in the LMNA gene, affecting the development and maintenance of the skin’s structure.

Question 6

What refers to one of the two identical copies of DNA that make up a replicated chromosome?
A.Chromatid
B.Chromatin
C.Nucleolus
D.Gene

A single DNA molecule wrapped around proteins called histones, forms a structure known as??
A.Chromatid
B.Chromatin
C.Nucleosome
D.Nucelotide

During cell division, each chromosome replicates to form two chromatids that are held together at a region called the centromere. These chromatids are not exact copies of each other, containing the different genetic information
True or false

What refers to one of the two identical copies of DNA that make up a replicated chromosome?

1. During which phase of the cell cycle does DNA replication occur?
   A. G1 phase
   B. S phase
   C. G2 phase
   D. M phase
   
   2. After DNA replication in the S phase of the cell cycle, each chromosome consists of two sister chromatids. What holds these sister chromatids together?
      A. Telomere
      B. Histone
      C. Centromere
      D. Nucleosome
   3. What is the function of sister chromatids during cell division?
      A. To replicate DNA
      B. To separate and form individual chromosomes
      C. To protect DNA from damage
      D. To initiate cell signaling pathways

Here are two more difficult questions based on the provided information:

4. Which specific phase of mitosis is characterized by the separation of sister chromatids, ensuring each daughter cell receives an identical set of chromosomes?
   A. Prophase
   B. Metaphase
   C. Anaphase
   D. Telophase
5. What molecular process is directly responsible for the separation of sister chromatids during anaphase?
   A. DNA polymerase activity
   B. Spindle fiber depolymerization
   C. Proteolytic cleavage of cohesin proteins
   D. Telomerase elongation
6. Which enzyme complex is crucial for triggering the transition from metaphase to anaphase by targeting securin for degradation, thereby allowing the separation of sister chromatids?
   A. DNA helicase
   B. Cyclin-dependent kinase (CDK)
   C. Anaphase-promoting complex (APC/C)
   D. Topoisomerase
   7. If a cell fails to properly attach its chromosomes to the spindle fibers during metaphase, which checkpoint will prevent it from proceeding to anaphase?
      A. G1/S checkpoint
      B. G2/M checkpoint
      C. Spindle assembly checkpoint (SAC)
      D. DNA damage checkpoint

What is a nucleosome

Answer 6

A chromatid is one of the two identical copies of DNA that make up a replicated chromosome. A chromatid consists of a single DNA molecule wrapped around proteins called histones, forming a structure known as chromatin. During cell division, each chromosome replicates to form two chromatids that are held together at a region called the centromere. These chromatids are exact copies of each other, containing the same genetic information

Chromatin
Complex of DNA and protein that make up the chromosome. Chromatin refers to the complex of DNA, RNA, and proteins found in the nucleus of eukaryotic cells.
• Composition: It consists of DNA molecules tightly coiled around histone proteins, forming nucleosomes. These nucleosomes further coil and condense to form chromatin fibers.

A chromatid is one of the two identical copies of DNA that make up a replicated chromosome.
• Formation: After DNA replication in the S phase of the cell cycle, each chromosome consists of two sister chromatids, which are held together at the centromere.
• Function: During cell division (mitosis or meiosis), chromatids separate to form individual chromosomes, ensuring that each daughter cell receives an identical set of genetic material.

Key Differences:

•	Structure: Chromatin is the condensed form of DNA in the nucleus, while chromatid refers to the duplicated form of a chromosome

chromatin is the general term for the DNA-protein complex found in the nucleus, while chromatids are specific structures formed during the cell division process.

Nucleosomes are the building blocks of chromatin, which compacts DNA.
• Chromatin organizes into chromosomes during cell division.
• Each chromatid is one of the two identical halves of a duplicated chromosome before they are separated during division.

Chromatin allows for the efficient packaging of DNA while regulating access to the DNA for processes such as transcription, replication, and repair.
And nucleosome will help the chromatin condense during cell division

A chromatid forms when the cell prepares for division (during mitosis or meiosis).
• During DNA replication, chromatin is duplicated, and each chromosome now consists of two identical sister chromatids.
• Each chromatid is made of tightly packed chromatin, and within that chromatin, the DNA is organized into nucleosomes.

The condensing of chromatin doesn’t mean it’s composed solely of heterochromatin during cell division.

Nn
Chromosome
Separate pieces of DNA in a cell made of chromatin (condensed form).
Chromatid
Sister chromatids are identical pieces of DNA held together by a centromere and pulled apart during cell division to make new identical chromosomes in the newly made cells.

1. During which phase of the cell cycle does DNA replication occur?
   A. G1 phase
   B. S phase
   C. G2 phase
   D. M phase
   Answer: B. S phase
   
   2. After DNA replication in the S phase of the cell cycle, each chromosome consists of two sister chromatids. What holds these sister chromatids together?
      A. Telomere
      B. Histone
      C. Centromere
      D. Nucleosome
      Answer: C. Centromere
   3. What is the function of sister chromatids during cell division?
      A. To replicate DNA
      B. To separate and form individual chromosomes
      C. To protect DNA from damage
      D. To initiate cell signaling pathways
      Answer: B. To separate and form individual chromosomes

Here are two more difficult questions based on the provided information:

4. Which specific phase of mitosis is characterized by the separation of sister chromatids, ensuring each daughter cell receives an identical set of chromosomes?
   A. Prophase
   B. Metaphase
   C. Anaphase
   D. TelophaseAnswer: C. Anaphase
5. What molecular process is directly responsible for the separation of sister chromatids during anaphase?
   A. DNA polymerase activity
   B. Spindle fiber depolymerization
   C. Proteolytic cleavage of cohesin proteins
   D. Telomerase elongationAnswer: C. Proteolytic cleavage of cohesin proteins
6. Which enzyme complex is crucial for triggering the transition from metaphase to anaphase by targeting securin for degradation, thereby allowing the separation of sister chromatids?
   A. DNA helicase
   B. Cyclin-dependent kinase (CDK)
   C. Anaphase-promoting complex (APC/C)
   D. Topoisomerase
   Answer: C. Anaphase-promoting complex (APC/C)
   7. If a cell fails to properly attach its chromosomes to the spindle fibers during metaphase, which checkpoint will prevent it from proceeding to anaphase?
      A. G1/S checkpoint
      B. G2/M checkpoint
      C. Spindle assembly checkpoint (SAC)
      D. DNA damage checkpoint
      Answer: C. Spindle assembly checkpoint (SAC)

These questions focus on more specific details of cell division, particularly the phases and molecular mechanisms involved. Let me know if you need more questions or additional explanations!

Question 7

What is the nucleolus and what is its function
Is the nucleolus membrane bound

mature rRNA molecules that form the core components of what subunits?

The nucleolus is the site where what is transcribed into precursor rRNA molecules.
How are small and large ribosomal sub units formed?
After precursor rRNA undergoes processing and modification in the nucleus, what does it produce?

Answer 7

The nucleolus is a distinct structure found within the nucleus of eukaryotic cells. It is primarily responsible for the synthesis and assembly of ribosomal RNA (rRNA) and the initial assembly of ribosomal subunits.
rRNA combines with small proteins to form the ribosomes.
3. Function:
- rRNA Synthesis: The nucleolus is the site where ribosomal DNA (rDNA) is transcribed into precursor rRNA molecules.
- rRNA Processing: Precursor rRNA undergoes processing and modification within the nucleolus to produce mature rRNA molecules that form the core components of ribosomal subunits.
- Ribosome Assembly: Ribosomal proteins synthesized in the cytoplasm are imported into the nucleus, where they combine with rRNA to form small and large ribosomal subunits. This initial assembly of ribosomal subunits occurs within the nucleolus

Here are some key points about the nucleolus:

1. Location: Typically, there is one nucleolus per nucleus, although some cells may have multiple nucleoli. It is a prominent structure that can be observed under a microscope.
2. Composition: The nucleolus is not membrane-bound like other organelles. Instead, it is a dense region within the nucleus composed of DNA, RNA, and proteins

Question 8

State two types of chromatins and define them
Where is each type found in the cell?
Which of the chromatins is involved in maintaining chromosome structure and stability and is less accessible to transcriptional machinery, restricting gene expression?

Answer 8

Chromatin is broadly categorized into two main types based on its structural state and accessibility to cellular machinery:

1. Euchromatin:
   
   • Structure: Euchromatin is less condensed and appears more dispersed in the nucleus during interphase. It is loose type of chromatin. This means the DNA doesn’t wrap around the histone proteins tightly. Those ones are usually found in the center of the nucleus.
2. Heterochromatin:
   
   • Structure: Heterochromatin is highly condensed and appears more compact under the microscope.DNA wraps around the histone proteins and it is located near or closer to the nuclear envelope
   • Function: It contains genes that are typically inactive or only sporadically active. Heterochromatin is involved in maintaining chromosome structure and stability. It is less accessible to transcriptional machinery, restricting gene expression.

These two types of chromatin are dynamic and can interconvert in response to cellular needs and environmental cues. The balance between euchromatin and heterochromatin plays a critical role in regulating gene expression, cellular differentiation, and maintaining genomic integrity.

Question 9

State four functions of the cytoplasm

Answer 9

Functions of the cytoplasm

Contains organelles

Site of chemical reactions and protein synthesis

Stores energy in the form of triglycerides or glycogen in structures called inclusions.

Stores molecules to be secreted in secretory vesicles.

Question 10

What part of the cell is referred to as the phospholipid bilayer ?
What is this part made up of?
What is a phospholipid bilayer

Answer 10

Cell membrane.

Cells have a cell membrane made of phosphate, proteins, and lipids

A phospholipid bilayer because it has the polar side and the non polar side.
Phospholipid part and fatty acid part.

Each phospholipid molecule in the bilayer has two parts:

1. Polar (Hydrophilic) Head: This part is attracted to water. It consists of a phosphate group and glycerol. Because it is polar, it interacts well with water and other polar molecules.
2. Non-Polar (Hydrophobic) Tails: These are fatty acid chains that repel water. There are usually two long fatty acid chains attached to the glycerol backbone. These tails face inward, away from water, and towards each other, forming the interior of the bilayer.

Hydrophobic tails :They point inward, facing each other within the interior of the lipid bilayer.
Hydrophilic heads: They point outward, facing the aqueous environments both inside and outside the cell.

The structure of the phospholipid bilayer allows it to form a stable barrier in aqueous environments, with the hydrophilic heads facing the external and internal aqueous environments of the cell and the hydrophobic tails facing each other in the middle of the bilayer.

Question 11

What is the function of cholesterol in the cell membrane
What are the two types of cell membrane proteins ?
Which of the two types is invovled in signaling and which is invovled in transportation of molecules

Answer 11

It gives the cell its fluidity. So too much cholesterol makes the cell rigid and too little makes it more fluid.

Integral proteins (span the whole length of the cell membrane) and peripheral proteins (don’t span the whole length of the cell membrane)

Integral Proteins**:
- These proteins span the entire length of the cell membrane.
- They are embedded within the phospholipid bilayer and can have one or more segments that traverse the membrane.
- Integral proteins often function as channels, transporters, or receptors, facilitating the movement of substances across the membrane or transmitting signals.

Remember integral means important so integral transporters then for
Peripheral to remember its signaling, peripheral signals.
2. Peripheral Proteins:
- These proteins do not span the entire membrane.
- They are typically attached to the exterior or interior surfaces of the membrane, often bound to integral proteins or to the polar heads of phospholipids.
- Peripheral proteins play roles in signaling, maintaining the cell’s shape, and anchoring the membrane to the cytoskeleton.

Question 12

State three functions of the cell membrane
Eukaryotes have cell membrane and cell wall. True or false

Answer 12

Cell membrane separates the components of a cell from its environment—surrounds the cell.
“Gatekeeper” of the cell—regulates the flow of materials into and out of cell.—selectively permeable
Cell membrane helps cells maintain homeostasis—stable internal balance

Prokaryotes (have a cell wall + cell membrane)
Eukaryotes:
a) Animal cells (cell membrane only)
b) Plant cells (cell membrane + cell wall)

Question 13

What is the rough ER. What is the function of the rough endoplasmic reticulum ?
Where is glucose 6 phosphatase located in the rough ER? What is the importance of this glucose 6 phosphatase ?

Answer 13

The rough ER is a Filamentous network that has a rough surface. The Membrane of the filamentous network has glucose 6 phosphatase making it important in glycogen breakdown(breaking the phosphate from the glucose on the sixth carbon so you get glucose only ). This glucose 6 phosphatase enzyme is crucial in the final step of glycogenolysis (glycogen breakdown) and gluconeogenesis (glucose production).
- It catalyzes the hydrolysis of glucose-6-phosphate to glucose and inorganic phosphate.
- This reaction occurs in the lumen of the ER, and the produced glucose is then transported into the cytoplasm and subsequently released into the bloodstream.
The presence of glucose-6-phosphatase in the rough ER is particularly important in liver cells (hepatocytes) and kidney cells, where it helps regulate blood glucose levels, especially during fasting or strenuous activity.

It’s rough cuz it has ribosomes attached to the surface of the filaments. Rough ER Bears ribosomes which function as site for protein synthesis

Site of protein synthesis, modification(example is formation of glycoproteins) and folding.

Question 14

What is the function of the smooth endoplasmic reticulum
Which enzyme in the liver is mostly found in the smooth ER?

Answer 14

Smooth endoplasmic reticulum:
Site for lipid synthesis(fatty acids,cholesterol)
Stores calcium ions
Detoxify blood

The CYP450 enzyme(for the bio transformation or metabolism of materials absorbed into the cell) is mostly found in the smooth ER.

Question 15

What is the sarcoplasmic reticulum? Where is it usually found ?

Answer 15

The sarcoplasmic reticulum (SR) is responsible for the storage of calcium ions (Ca²⁺).

• The SR is a specialized type of smooth endoplasmic reticulum found in muscle cells.
• It plays a critical role in muscle contraction and relaxation by regulating the concentration of calcium ions within the muscle fiber.
• When a muscle cell is stimulated to contract, calcium ions are released from the SR into the cytoplasm, initiating the interaction between actin and myosin filaments necessary for contraction.
• Following contraction, calcium ions are pumped back into the SR, allowing the muscle to relax.

The efficient storage and release of calcium by the sarcoplasmic reticulum are essential for the proper functioning of muscle tissue.

So it’s usually in the muscles

Question 16

State two functions of the Golgi apparatus
What is glycosylation
What type of glycosylation is done in the Golgi apparatus and what type is done in the endoplasmic reticulum?

Answer 16

Golgi apparatus
-Processes molecules synthesized in the endoplasmic reticulum and prepares them for transport to their final destination
-Packages molecules that come from the ER into vesicles and directs the vesicles to their appropriate location(either into membrane or out of the cell)
-does modification (example is glycosylation)

Glycosylation is a biochemical process where a carbohydrate (glycan) is covalently attached to a protein, lipid, or other organic molecule. This modification plays a crucial role in various cellular functions, including protein folding, stability, and cell signaling.

There are two main types of glycosylation:

1. N-linked Glycosylation:
   
   • This process attaches a carbohydrate to the nitrogen atom (N) of an asparagine amino acid residue within a protein.
   • It occurs in the endoplasmic reticulum (ER) and is further modified in the Golgi apparatus.
   • N-linked glycosylation is essential for proper protein folding and quality control within the ER.
2. O-linked Glycosylation:
   
   • In this type, the carbohydrate is attached to the oxygen atom (O) of serine or threonine amino acid residues.
   • This process occurs mainly in the Golgi apparatus.
   • O-linked glycosylation affects the stability and function of proteins and is involved in forming the extracellular matrix and mucins.

Question 17

State two functions of the Golgi apparatus
What is glycosylation
What type of glycosylation is done in the Golgi apparatus and what type is done in the endoplasmic reticulum?

Answer 17

Golgi apparatus
-Processes molecules synthesized in the endoplasmic reticulum and prepares them for transport to their final destination
-Packages molecules that come from the ER into vesicles and directs the vesicles to their appropriate location(either into membrane or out of the cell)
-does modification (example is glycosylation)

Glycosylation is a biochemical process where a carbohydrate (glycan) is covalently attached to a protein, lipid, or other organic molecule. This modification plays a crucial role in various cellular functions, including protein folding, stability, and cell signaling.

There are two main types of glycosylation:

1. N-linked Glycosylation:
   
   • This process attaches a carbohydrate to the nitrogen atom (N) of an asparagine amino acid residue within a protein.
   • It occurs in the endoplasmic reticulum (ER) and is further modified in the Golgi apparatus.
   • N-linked glycosylation is essential for proper protein folding and quality control within the ER.
2. O-linked Glycosylation:
   
   • In this type, the carbohydrate is attached to the oxygen atom (O) of serine or threonine amino acid residues.
   • This process occurs mainly in the Golgi apparatus.
   • O-linked glycosylation affects the stability and function of proteins and is involved in forming the extracellular matrix and mucins.

Question 18

What is the function of the mitochondria
What processes occur in the mitochondria?
Does the mitochondria have its own DNA?
Which part of the mitochondria is for energy production? (NB: take note of where the processes that produce energy for the cell take place in the cell. Some occur in the cytoplasm, some the mitochondrial matrix, some start in one place and ends somewhere else)

Answer 18

Mitochondria
Produces energy for the cell in the form of ATP
It has an inner and an outer part. It has a mitochondrial matrix. The mitochondria has its own DNA and this DNA is from the mother. It is called mitochondrial DNA

Yes, the mitochondrial matrix is a crucial site for energy production within the cell:processes occurring in the mitochondrial matrix;

1. **Krebs Cycle (Citric Acid Cycle, tricarboxylic acid (TCA) cycle)
   
   • The matrix is where the Krebs cycle takes place, a series of enzymatic reactions that produce electron carriers (NADH and FADH₂) by oxidizing acetyl-CoA derived from carbohydrates, fats, and proteins.
2. Electron Transport Chain (ETC) and Oxidative Phosphorylation:
   
   • The inner mitochondrial membrane, which surrounds the matrix, hosts the electron transport chain. NADH and FADH₂ generated in the matrix donate electrons to the ETC.
   • The flow of electrons through the ETC generates a proton gradient across the inner mitochondrial membrane.
3. ATP Synthesis:
   
   • The proton gradient drives the synthesis of ATP by ATP synthase, which is also embedded in the inner mitochondrial membrane but extends into the matrix.
   • ATP synthesis occurs in the matrix, where ADP and inorganic phosphate are combined to form ATP.
4. Urea Cycle:
   
   • Location: Primarily in the liver, with steps occurring in both the mitochondrial matrix and the cytoplasm.
   • Function: The urea cycle converts toxic ammonia to urea, which is then excreted in urine. This process is vital for the detoxification of ammonia generated during amino acid metabolism.
5. Heme Synthesis:
   
   • Location: Begins in the mitochondrial matrix and continues in the cytoplasm.
   • Function: Heme synthesis is the process by which heme, an essential component of hemoglobin, myoglobin, and various cytochromes, is produced. It involves the production of protoporphyrin IX, which combines with iron to form heme.
6. Gluconeogenesis:
   
   • Location: Mainly in the liver and, to a lesser extent, in the kidneys. It occurs in both the cytoplasm and the mitochondrial matrix.
   • Function: Gluconeogenesis is the synthesis of glucose from non-carbohydrate precursors such as lactate, glycerol, and glucogenic amino acids. This process is critical during fasting or intense exercise to maintain blood glucose levels.
7. Ketogenesis:
   
   • Location: Mitochondrial matrix of liver cells.
   • Function: Ketogenesis is the production of ketone bodies (acetoacetate, β-hydroxybutyrate, and acetone) from acetyl-CoA. Ketone bodies are an important alternative energy source during prolonged fasting, carbohydrate restriction, or intense exercise.

Each of these metabolic processes plays a crucial role in maintaining energy balance and homeostasis in the body.

In summary, the mitochondrial matrix is essential for the Krebs cycle and the production of electron carriers, which are crucial for ATP generation through the electron transport chain and oxidative phosphorylation.

Question 19

Where does Glycolysis occur in the cell?
How many ATP does glycolysis produce?
How many ATP does Citric acid cycle produce?
What is the net gain of ATP in glycolysis

Answer 19

In The cytoplasm not the mitochondrial matrix

1. Glycolysis:
   
   • Location: Cytoplasm
   • Function: Glycolysis is the breakdown of glucose into pyruvate, producing a net gain of 2 ATP and 2 NADH molecules. It is the first step in both aerobic and anaerobic respiration.

The process that produces a net gain of 4 ATP molecules per glucose molecule is substrate-level phosphorylation during the citric acid cycle (Krebs cycle).

Here’s a summary of the ATP production:

•	Glycolysis: Net gain of 2 ATP.
•	Citric Acid Cycle: Produces 2 ATP (or GTP, depending on the cell type) per cycle. Since the cycle runs twice per glucose molecule, it results in a total of 4 ATP (or 4 GTP) produced per glucose.

In glycolysis, the total production is 4 ATP, but since 2 ATP are used initially, the net gain is 2 ATP.

Glycolysis produces a net gain of 2 ATP molecules per molecule of glucose. Here’s a brief breakdown:

• Initial Investment: 2 ATP molecules are used in the early steps of glycolysis.
• Production: 4 ATP molecules are produced in the later steps of glycolysis.

Thus, the net gain of ATP is ( 4 \, \text{(produced)} - 2 \, \text{(used)} = 2 ) ATP molecules.

Yes, the net gain from the citric acid cycle (Krebs cycle) is 2 ATP (or GTP) per glucose molecule. Since each glucose molecule produces two acetyl-CoA molecules, the citric acid cycle runs twice, leading to a total of 4 ATP (or GTP) produced per glucose molecule.

Here’s the breakdown:
- Each cycle (per acetyl-CoA) produces: 1 ATP (or GTP)
- Total for two cycles (per glucose): 2 ATP (or GTP)

So, the net gain is 2 ATP per glucose molecule from the citric acid cycle, but 4 ATP (or GTP) are produced in total due to the two cycles.

Question 20

Mrna and tRNA carry info from the nucleus to the ribosomes then protein synthesis goes on and then the proteins are shipped to where they gotta go to.
True or false
What are the functions of lysosomes?
What’s the difference between autophagy and autolysis

Answer 20

True
Lysosomes Contain hydrolytic enzymes (examples are lipase,nuclease,protease,glucosidases)that degrade cellular debris for recycling and excretion of waste
Enzymes also help degrade endocytosed vesicles

Lysosomes are also involved in autophagy and autolysis. Here are the summarized differences between autophagy and autolysis:

1. Autophagy:
   
   • Definition: Autophagy is a cellular process where cells degrade and recycle damaged or unnecessary components within themselves.
   • Mechanism: It involves the formation of autophagosomes that engulf cellular material, which then fuse with lysosomes to form autolysosomes where degradation occurs.
   • Purpose: Autophagy helps maintain cellular homeostasis, remove damaged organelles, and provide nutrients during stress or starvation.
   • Context: It is a regulated process essential for cellular health and survival.
2. Autolysis:
   
   • Definition: Autolysis refers to the process of self-digestion that occurs at a cellular level, typically post-mortem or in certain types of necrosis.
   • Cause: It occurs due to the release of lysosomal enzymes into the cytoplasm when cell membrane integrity is compromised.
   • Outcome: Autolysis leads to the breakdown of cellular components and tissues, contributing to decomposition or tissue damage.
   • Context: While autolysis post-mortem is a natural process contributing to decomposition, autolysis in necrosis involves similar mechanisms but occurs in living cells due to pathological conditions.

In essence, autophagy is a controlled cellular process for maintaining cellular health and function, while autolysis involves the uncontrolled release of lysosomal enzymes leading to self-digestion, either post-mortem or in pathological states like necrosis.

Question 21

What three functions of Peroxisomes
What two important enzymes does Peroxisomes contain?
Which of the enzymes breakdown hydrogen peroxide into water and oxygen?
What is a byproduct of various metabolic processes and can be toxic if it accumulates within cells?
A. Acetaldehyde
B. Urea
C. Lactic Acid
D. Hydrogen Peroxide

Answer 21

Peroxisomes :
Function in degradation of molecules such as amino acids, fatty acids and foreign substances
Contains catalase and oxidases which removes free oxygen radicals

Peroxisomes are specialized organelles found in eukaryotic cells, responsible for various metabolic functions, particularly involving oxidation reactions. Here’s how peroxisomes, catalase, and oxidases work to remove free oxygen radicals:

1. Function of Peroxisomes:
   
   • Peroxisomes are involved in lipid metabolism(while endoplasmic reticulum does lipid synthesis specifically smooth ER),detoxification of harmful substances, and the metabolism of reactive oxygen species (ROS).
   • They contain enzymes such as catalase and various oxidases that participate in oxidative reactions.
2. Catalase in Peroxisomes:
   
   • Role: Catalase is a key enzyme found in peroxisomes that catalyzes the breakdown of hydrogen peroxide (H₂O₂) into water (H₂O) and oxygen (O₂).
   • Importance: Hydrogen peroxide is a byproduct of various metabolic processes and can be toxic if it accumulates within cells. Catalase helps neutralize hydrogen peroxide, preventing cellular damage caused by oxidative stress.
3. Oxidases in Peroxisomes:
   
   • Types: Peroxisomes contain different types of oxidases, including flavin oxidases and D-amino acid oxidases.
   • Functions: These oxidases participate in the oxidation of various substrates, generating hydrogen peroxide as a product. However, this hydrogen peroxide is then efficiently broken down by catalase within the peroxisome itself.
4. Free Oxygen Radicals:
   
   • Formation: Free oxygen radicals (or reactive oxygen species, ROS) can be generated as byproducts of cellular metabolism, especially during oxidative processes.
   • Removal: Catalase and other peroxisomal enzymes play a crucial role in detoxifying and neutralizing ROS like hydrogen peroxide, thereby protecting cells from oxidative damage.

In summary, peroxisomes are organelles that house enzymes such as catalase and oxidases, which work together to detoxify harmful substances like hydrogen peroxide and mitigate oxidative stress in cells. This function is essential for maintaining cellular health and preventing oxidative damage associated with aging, disease, and environmental factors.

Association with Antioxidation

Since peroxisomes are already associated with antioxidation in your mind, link each function to the concept of protection:

•	Lipid metabolism: Protects by processing essential fats.
•	Amino acids degradation: Protects by breaking down proteins for energy.
•	Detoxification: Directly protects against toxins.
•	fatty acids degradation: Protects by managing energy sources.

Which of the following byproducts of various metabolic processes is known to be toxic if it accumulates within cells due to its role in oxidative stress?

A. Acetaldehyde
B. Urea
C. Lactic Acid
D. Hydrogen Peroxide

Answer: D. Hydrogen Peroxide

Question 22

Which organelle Directs the development of mitotic spindle during cell division?
Where is this organelle found in the animal cell?

Answer 22

Centrioles are cylindrical structures found in animal cells, typically located near the nucleus within a region called the centrosome(different from centromere which holds two sister chromatids together. Remember it this way, the mother holds the home together so centroMERE. Ma mere which is mother in French) . They play crucial roles in cell division (mitosis and meiosis) by organizing the mitotic spindle, which is essential for the accurate segregation of chromosomes into daughter cells.

Centrioles:
Direct the development of mitotic spindle during cell division

Question 23

What is the function of the cytoskeleton of the cell
State the three different types of filaments in the cytoskeleton,their structures and then their functions

Answer 23

Cytoskeleton
Provides skeletal framework for the cell (mechanical support)

Cytoskeleton of human body has intermediate filaments,micro filaments and macro filaments

In the human body, the cytoskeleton is a complex network of protein filaments that provides structural support, facilitates cellular movement, and helps maintain cell shape. It consists primarily of three types of protein filaments: intermediate filaments, microfilaments (actin filaments), and microtubules (not macro filaments, which isn’t a widely recognized term in this context). Here’s a brief overview of each:

1. Intermediate Filaments:
   
   • Structure: Intermediate filaments are relatively stable and are composed of various fibrous proteins depending on the cell type. Examples include keratins in epithelial cells and vimentin in connective tissue cells.
   • Function: They provide mechanical strength to cells and tissues, helping to maintain cell shape and resist mechanical stress.it anchors the cell to the extracellular matrix to help maintain the cell shape.
2. Microfilaments (Actin Filaments):
   
   • Structure: Microfilaments are the thinnest filaments of the cytoskeleton, composed primarily of actin protein subunits arranged in a helical structure.
   • Function: Actin filaments are involved in various cellular processes, including muscle contraction, cell division (cytokinesis), cell movement (e.g., diapedesis,helps in engulfing bacteria in phagocytosis,crawling and contraction), and the maintenance of cell shape.
3. Microtubules:
   
   • Structure: Microtubules are hollow tubes made of tubulin protein subunits arranged in a cylindrical structure.
   • Function: They serve as tracks for intracellular transport, guiding the movement of organelles and vesicles within the cell. Microtubules also play a critical role in chromosome segregation during cell division and contribute to the structural support of cilia and flagella.
     Types of motor proteins that work with micro tubules include kinesins and dyneins. They are transport proteins. In splitting sister chromatids during mitosis, there are specific proteins that hold the middle piece to be able to split them. The proteins are the kinins and dinins.
     These three types of protein filaments work together to maintain the structural integrity of cells, facilitate cellular movements and interactions, and ensure the proper functioning of cellular processes essential for life and function in the human body.

Question 24

Under the general cellular transport mechanisms, state the two main types with examples underneath

Answer 24

Active transport:
Energy is needed cuz molecules are going against the concentration gradient or electrochemical gradient. It includes protein pumps,endocytosis and exocytosis. These use active transport

Passive transport:
diffusion
Facilitated diffusion (uses proteins not energy to push particles across)
Osmosis

Question 25

What is diffusion?

Answer 25

Diffusion is the movement of small particles across a selectively permeable membrane like the cell membrane until equilibrium is reached.

These particles move from an area of high concentration to an area of low concentration.

expample is spraying perfume and the perfume moves to an area where there was no perfume. It has moved from where it was concentrated to where it’s not concentrated so high to low

Question 26

By what means of transport do each of these processes occur?(the means of transport are : osmosis,diffusion, active transport,etc):
1. Gaseous exchange(oxygen and carbon dioxide are lipid soluble)
2.Absorption of digested nutrients
3.Propagation of nerve impulses
4.Movement of hormones and other metabolites towards their target organ.

Answer 26

-
All these physiological processes occur by diffusion

Gaseous exchange(oxygen and carbon dioxide are lipid soluble)
-Absorption of digested nutrients
-Propagation of nerve impulses
-Movement of hormones and other metabolites towards their target organ.

Question 27

State five factors affecting rate of diffusion. (They are grouped under molecular factors(3),membrane related factors (1) and gradients related factors(2) )

Questions come from here too a lot

Answer 27

Molecular:
Lipid solubility(more lipid soluble molecules diffuse into the cell quickly)
Molecular size and weight(smaller molecular weights and size diffuse more quickly)
Temperature(Higher temperatures accelerate diffusion rates because molecules move more rapidly)

Membrane related:
Surface area(A larger surface area enhances the rate of diffusion by allowing more molecules to pass through the membrane simultaneously)

Concentration gradient(A concentration gradient refers to the difference in solute concentration across a membrane.
- Impact on Diffusion: The steeper the concentration gradient (i.e., the greater the difference in concentration between two sides of the membrane), the faster the rate of diffusion.)

Electrical gradient ( the electrical gradient refers to the difference in electrical charge (voltage) across a biological membrane that influences the movement of ions:The electrical gradient complements the concentration gradient in influencing ion movement. The electrochemical gradient takes into account both the concentration gradient and the electrical gradient of ions across the membrane.
- Direction of Movement: Ions will move across the membrane in a manner that tends to equalize both their concentration and electrical potentials between the two sides of the membrane
- Positively charged ions (cations) move towards areas of lower positive charge (more negative inside the cell), while negatively charged ions (anions) move towards areas of higher positive charge (more positive inside the cell

Question 28

What is facilitated diffusion
What are protein channels

Answer 28

Facilitated diffusion requires the help of carrier and channel proteins
These particles move from an area of high concentration to an area of low concentration.
Facilitated diffusion is the movement of larger molecules like glucose through the cell membrane – larger molecules must be “helped”.
Proteins in the cell membrane form channels for large molecules to pass through.
Facilitated diffusion requires the help of carrier and channel proteins
These particles move from an area of high concentration to an area of low concentration.
Proteins that form channels (pores) are called protein channels

Question 29

Between Carrier proteins and channel proteins, which work by facilitating facilitated diffusion, a type of passive transport where molecules move down their concentration gradient (from high to low concentration)?

Between carrier and channel proteins, which undergoes a conformational change when an ion or molecule binds to the binding site on this protein?

Explain how carrier proteins work.
Explain how channel proteins work

Which type of proteins facilitate faster diffusion rates?

Answer 29

1. Carrier Proteins in Diffusion:
   
   • Mechanism: Carrier proteins facilitate facilitated diffusion, a type of passive transport where molecules move down their concentration gradient (from high to low concentration).
   • Process:
     
     • A molecule or ion binds to the specific binding site on the carrier protein located on one side of the membrane.
     • The carrier protein undergoes a conformational change, transferring the bound molecule or ion across the membrane to the other side.
     • The molecule or ion is released from the carrier protein, which returns to its original conformation, ready to transport another molecule.
   • Examples: Glucose transporters (e.g., GLUT proteins) and amino acid transporters utilize carrier proteins to facilitate their movement across cell membranes.
2. Channel Proteins in Diffusion:
   
   • Mechanism: Channel proteins facilitate passive diffusion by forming aqueous pores or channels through the membrane.
   • Process:
     
     • Channel proteins are selective based on size, charge, or other chemical properties, allowing specific ions or molecules to pass through.
     • Substances move through the channel down their electrochemical gradient, without requiring energy input (passive transport).
     • The rate of diffusion through channel proteins is typically faster compared to carrier proteins, as it depends on the size of the channel and the concentration gradient of the substance.
   • Examples: Ion channels such as sodium channels, potassium channels, and chloride channels are examples of channel proteins that allow ions to diffuse across cell membranes.

Comparison:

• Specificity: Carrier proteins exhibit specificity for their substrate molecules or ions, binding and transporting them across the membrane. Channel proteins are selective based on size and charge, allowing only certain substances to pass through.
• Mechanism: Carrier proteins undergo conformational changes to transport substances, while channel proteins provide a direct pathway (channel) for passive diffusion.
• Rate of Diffusion: Channel proteins generally facilitate faster diffusion rates compared to carrier proteins, as they provide a continuous pathway for molecules or ions to move across the membrane.

In summary, both carrier proteins and channel proteins facilitate the movement of molecules and ions across membranes through diffusion. Carrier proteins are involved in facilitated diffusion by binding to specific molecules and undergoing conformational changes, while channel proteins form pores that allow substances to passively diffuse across the membrane based on their electrochemical gradient.

Carrier Proteins:
- Function: Transport specific molecules (such as glucose, amino acids, and ions) across cell membranes.
- Mechanism: Bind to their substrate, undergo conformational changes, and facilitate transport across the membrane.
- Examples: GLUT (glucose transporter proteins) proteins (for glucose), amino acid transporters, and ion transporters like the sodium-potassium pump.

Channel Proteins:
- Function: Form pores or channels in membranes for ions or water to pass through.
- Mechanism: Provide a pathway for passive diffusion based on size, charge, and selectivity.
- Examples: Ion channels (e.g., sodium and potassium channels) and aquaporins (for water transport).

Question 30

Apart from energy, what else can active transport use in transporting stuff?
Give examples of this thing
Carrier proteins don’t need energy from ATP hydrolysis to carry out their work. True or false?

Answer 30

Carrier proteins

Active transport processes primarily involve carrier proteins that use the energy derived from ATP hydrolysis to move molecules or ions against their concentration gradients across biological membranes

Active transport primarily utilizes carrier proteins that are specifically designed to transport molecules or ions against their concentration gradients using energy from ATP hydrolysis. These carrier proteins include:

1. Sodium-Potassium Pump (Na+/K+ ATPase):
   
   • Function: Actively transports three sodium ions (Na+) out of the cell and two potassium ions (K+) into the cell per ATP hydrolyzed.
   • Role: Maintains cell volume, establishes an electrochemical gradient, and supports nerve signal transmission.
   • Location: Found in the plasma membranes of most animal cells.
2. Calcium Pump (Ca2+ ATPase):
   
   • Function: Actively transports calcium ions (Ca2+) out of the cytoplasm across cell membranes against their concentration gradient.
   • Role: Regulates calcium levels in cells, which is crucial for muscle contraction, signal transduction, and enzyme regulation.
   • Location: Found in the plasma membranes and membranes of organelles like the sarcoplasmic reticulum in muscle cells.
3. Proton Pump (H+ ATPase):
   
   • Function: Actively transports protons (H+) across membranes, creating a proton gradient.
   • Role: Involved in pH regulation, generating electrochemical gradients, and supporting nutrient uptake.
   • Location: Found in the plasma membranes of various cells, as well as in intracellular organelles like lysosomes and plant vacuoles.
4. ABC Transporters (ATP-Binding Cassette Transporters):
   
   • Function: Actively transport a wide range of substrates, including ions, sugars, lipids, and drugs, across membranes.
   • Mechanism: ATP hydrolysis provides energy for conformational changes that facilitate substrate transport.
   • Role: Involved in drug resistance, nutrient uptake, and removal of toxic substances.
   • Location: Found in various cellular membranes, including the plasma membrane and intracellular organelles.

ABC transporters have a characteristic structure with two nucleotide-binding domains (NBDs) and two transmembrane domains (TMDs). The ATP binding and hydrolysis in the NBDs provide the energy needed for the transport process.
• Examples: Notable examples include the multidrug resistance proteins (MDRs) that can pump out drugs from cells, contributing to drug resistance.

Question 31

The types of active transport are primary and secondary active transport. explain them
How is the body’s acidity regulated using active transport?
Sodium glucose transporter is an example of what type of secondary active transport?
What does moving against the concentration gradient mean?
What is moving down the concentration gradient mean
What is moving up the concentration gradient mean

Answer 31

Active transport refers to the movement of molecules or ions across a cell membrane against their concentration gradient, requiring energy usually derived from ATP hydrolysis.

There are several types of active transport mechanisms:

1. Primary Active Transport:
   
   • Mechanism: In primary active transport, energy from ATP hydrolysis directly powers the movement of molecules or ions against their concentration gradient.
   • Example: The sodium-potassium pump (Na+/K+ ATPase) actively transports sodium ions (Na+) (3sodium molecules) out of the cell and potassium ions (K+) (2 molecules of potassium) into the cell, maintaining ion gradients crucial for cellular functions.
2. Secondary Active Transport:
   
   • Mechanism: Secondary active transport utilizes the energy stored in an electrochemical gradient (usually of ions like sodium or hydrogen ions) to drive the transport of other molecules or ions against their concentration gradient. When something moves against a concentration gradient, it is moving up the gradient. This means it is moving from an area of lower concentration to an area of higher concentration, which typically requires energy input, such as ATP.
     In contrast, moving down the gradient would mean moving from an area of higher concentration to an area of lower concentration, which generally does not require energy and occurs via passive transport.
   • Types:
     
     • Symport (Cotransport): Transport of two different molecules or ions in the same direction across the membrane. One molecule moves down its concentration gradient, providing the energy to transport another molecule against its gradient. Example: SGLT (Sodium-Glucose Transporters or Symporter). This is behind ORS drink concept
     • Antiport (Countertransport): Transport of two different molecules or ions in opposite directions across the membrane. Example: Sodium-calcium exchanger (NCX), which exchanges sodium ions for calcium ions or sodium hydrogen antiporter which is usually found in the kidneys and is used to regulate acid base in blood. It does this by reabsorbing sodium and pushing out hydrogen from the blood and this regulates the body’s acidity

Here are clinically relevant examples of antiport and symport transporters:

Antiport Examples:

1. Sodium-Calcium Exchanger (NCX): This exchanger is crucial in cardiac muscle cells, where it helps regulate intracellular calcium levels, which is important for proper heart function.
2. Chloride-Bicarbonate Exchanger (AE1): Found in red blood cells and involved in maintaining acid-base balance by exchanging chloride ions and bicarbonate ions.
3. Sodium-Hydrogen Exchanger (NHE): Exchanges one sodium ion (Na+) inward for one hydrogen ion (H+) outward.

Symport Examples:

1. Sodium-Glucose Co-Transporter (SGLT): Found in the kidneys and intestines, this transporter is significant for glucose reabsorption. Inhibitors of SGLT2 (a subtype) are used to treat diabetes by promoting glucose excretion in urine.
2. Sodium-Iodide Symporter (NIS): Essential for thyroid function, it helps transport iodide into thyroid cells for the synthesis of thyroid hormones. Dysfunction can lead to thyroid disorders.
3. Sodium-Amino Acid Co-Transporters: These transporters are crucial for the absorption of amino acids from the gut, which is essential for nutrition and overall health.

Question 32

Calcium ATpase is found in which part of the cell?

Answer 32

Sarcoplasmic reticulum

Question 33

Which AT pase is the most common in the body?
What is E1 and E2 conformation in ion pumps?
Which side of the cell does E1 face (intracellular or Extracellular)

Which side of the cell does E2 face (intracellular or Extracellular)

Answer 33

Sodium potassium ATpase

The terms E1 and E2 refer to specific conformations or states of an ion pump, such as the sodium-potassium pump (Na+/K+ ATPase), during its function in active transport:

1. E1 Conformation:
   
   • Definition: The E1 conformation of the pump is characterized by its binding sites facing the intracellular side of the membrane.(intracellular because at this stage, it is not picking sodium from the inside)
   • Function: In this state, the pump has a high affinity for sodium ions (Na+), binding three Na+ ions from the cytoplasm.
   • Energy Consumption: ATP hydrolysis occurs at this stage to provide energy for the subsequent conformational change.
2. E2 Conformation:
   
   • Definition: The E2 conformation occurs after ATP is hydrolyzed, causing a conformational change in the pump.
   • Function: In the E2 state, the pump undergoes a change in its structure, causing the binding sites to face the extracellular side of the membrane.( Extracellular because at this conformation is where sodium is pumped out of the cell and potassium is pumped in)
   • Ion Release: This change leads to the release of sodium ions (Na+) to the outside of the cell.
   • Ion Binding: Simultaneously, the E2 state allows for the binding of two potassium ions (K+) from the of them Palest? Jahren

Question 34

Cell physiology:
Inorganic substances are ions
Organic substances are glucose amino acids fatty acids hormone enzymes
The above are solids in the body fluids

Hormones and enzymes are organic because they are primarily composed of carbon, hydrogen, oxygen, and often nitrogen and sulfur. These elements form the backbone of organic molecules, which are defined by the presence of carbon atoms.

When fluids are localized in particular parts of the body, they are trans cellular.

•	Interstitial fluid surrounds and bathes the cells in tissues.
•	Transcellular fluid is found in specific compartments, such as cerebrospinal fluid (CSF), synovial fluid (in joints), peritoneal fluid (in the abdominal cavity), and pleural fluid (around the lungs).

Transcellular fluid is separated from the interstitial fluid by epithelial or endothelial layers.

Lymph is Extracellular. Fluid in bones and cartilage is ECF
Plasma is ECF

Know where the substances are. ICF OR ECF??

Test substances or markers are used under experimental conditions.

Cell isn’t the basic unit of life.
It is the basic functional and structural unit of life but isn’t the basic unit of life.

It’s not the basic unit of life cuz there are atoms and molecules that are more basic. Just that they aren’t really functional.

2 major parts of the cell;
Cytoplasm
Nucleus

Nucleus- nuclear envelope,chromatin,nucleolus

The things in the cytoplasm can generally be divided into inclusions and organelles

Peroxisomes break down foreign substances and catalase removes free ROS

Organelles in the cell:

Diffusion occurs with or without a permeable membrane.
There should be concentration gradient between the two areas where the diffusion is to happen. Concentration gradient is difference in concentrations. So one must be higher than the other. If there is equilibrium, no diffusion will take place

If concentration gradient isn’t there or there is equilibrium, the electrical gradient or charges may be different and this will cause diffusion with regards to ions and nerve impulses.

Proteins that form channels or pores are called protein channels

Osmosis:water molecules from low to high across a semi permeable membrane

Depends on if it’s a solute making a move or solvent making a move

So the water molecules move from low solute conc to high solute conc and the water molecules move from high solvent to low solvent

Yes, that’s correct! Here’s how it works:

• Water molecules move from low solute concentration to high solute concentration: This means that water moves from an area where there is less solute (and thus more water) to an area where there is more solute (and thus less water). Water is moving to “dilute” the higher concentration of solute.
• Water molecules move from high solvent concentration to low solvent concentration: Since the solvent is water, this is just another way of saying the same thing. Water moves from where there is more water (high solvent concentration) to where there is less water (low solvent concentration).

In osmosis, the movement of water is driven by the concentration of solutes, but it is always the water (the solvent) that is moving, not the solutes themselves. This happens across a semi-permeable membrane that allows water to pass but not solutes. The goal is to balance the concentrations of solutes on both sides of the membrane.