biocell full q modified

Describe what is a cell and present its caractaristics

A cell is the structural and functional fundamental unit of life which is characterized by having self-regulation, self replication which means it gives its genetic information to daughter cells and has been through a long evolutionary process. A cell can be prokaryotic and eukaryotic. Human cells are eukaryotic.

Describe what types of cell there are

There are 2 main types of cells; Eukaryotes and Prokaryotes. Prokaryotic cells; bacteria, archaea. Eukaryotic cells; plants, animal, fungi.

Describe an organelle and specify its classification

An intercellular complex which has its special morphology and functions. Can be endomembrane bounded (peroxisome, endoplasmic reticulum , golgi, lysosome, nucleus) or can be non endomembrane bounded.

What are membranebound organelles and their main functions?

Peroxisome: oxidative reactions breakdown of long fatty acid chain. Neutralization of peroxides. lysosome: has digestive enzymes function is to digest macromolecules. Endoplasmic reticulum: storage of calcium, lipid and protein biosynthesis. Golgi: maturation, sorting and packaging also transporting. Nucleus: largest membrane bound organelle in mammals responsible to store genetic material, transcription of dna to rna.

What are organelles without membranes and their functions?

Cytoskeleton- network of fibrillary proteins, maintains cell shape enables movement and supports intracellular transport. Ribosome- Has smaller and larger subunits and in between subunits mRNA binds and translation occurs here. - protein synthesis. Proteasome- involved in digestion of cytosolic proteins. centrioles- which organizes the microtubule network and the mitotic spindle.

What are the main components of the eukaryotic cell?

cell membrane, cytoplasm (cytosol+organelles), nucleus, endomembranes.

What is a specialized cell (stem cell)?

Immature,undifferentiated, multipotent, self-renewing cells. When they are needed they can become mature, specialized cells by differentiation. They divide asymmetrically.

What are cytoplasmic inclusions?

lipid droplets and glycogen inclusions. They cannot perform metabolic activities.

Explain what is in vivo studies, their advantages and limitations

when cells/organs containing cells we want to study are approached in intact living organism. -> advant; results we obtain are close match for studies process at level of human organism. -> disad; results of experiments are difficult to interpret, because of the influences of other components in organisms.

Explain what is in vitro studies, their advantages and limitations

In vitro studies are when we are studying the cell isolated from the organism. The advantages ensure the rigorous control of the experiment. Limitations are one cannot guarantee that we'll obtain the same results as in vivo.

Define pre clinical studies and list their main components.

Preclinical studies aim to understand the mechanism of the diseases and target causes of the diseases. A new drug is always tested on animals to understand the efficacy and toxicity. genetic testing. protein studies. cell cultures. animal models.

Explain the role and importance of pre-clinical studies in drug development.

to understand mechanisms of diseases and not symptoms targeted by drugs. genetic testing (for specific mutations). protein study (structure of various disease causing proteins). cell cultures in vitro (testing new drugs on cells/tissues). animal models (testing new drugs on animals that have diseases).

What are the steps of permanent microscopy specimens

1.Harvesting 2. Fixation 3. Embedding 4. Sectioning 5. Staining 6. Mounting and Labeling.

Explain the method of fixation

To preserve the architecture of tissues+cells, prevent protein denaturation, tissue autolysis. Chemical fixation by using formaldehyde. Physical fixation by freezing. Fixation kills cells. but for EM we use glutaraldehyde and osmium tetroxide.

Talk about HE stains. Make sure you mention its components, results and mechanism of staining.

hemotoxylin- basic dye that binds to an acid (basophilic) purple ex:nucleus. eosine- acid dye that binds to a basic (acidophilic) pink ex:cytoplasm.

Name the types of light microscopy

microscopy- all about highlighting the contrast between intracellular structures. bright field - contrast is usually enhanced using conventional dyes. phase contrast - contrast is enhanced by differences in how light is refracted. fluorescent microscope.- contrast is enhanced by using fluorescent staining (florochrome).

How is the magnification power of a light microscope calculated?

magnification of objective lens x magnification of eye piece.

What are the common types of objectives used in light microscopy and their functions?

4x (locating). 10x (area of interest). 20x/40x (identify tissue type). 60x/100x (identify cell type).

What is the definition of resolution in light microscopy (LM)?

minimum distance at which two distinct points of a specimen appear as separate entities.

What factors does the resolution of a light microscope depend on?

refraction index, wavelengths and the optical characteristic of lens.

What is the physical limit of resolution in light microscopy

0.2𝜇 (diffraction limit).

How are the capabilities of electron microscopes measured?

magnification power, resolution.

Explain the principle of electron microscopy and define ultrastructure.

there’s a high voltage electron source which send electron beams and there are electromagnetic lenses electrons are projected to the detector and an image is recorded.

Explain the working principle of Transmission Electron Microscopy (TEM) and the meaning of electron dense and electron lucent areas.

-the e- beam is emitted continuously by a source which’s heated by a high voltage current. -it has a vacuum inside so that e- won’t collide with air molecules. -electromagnetic lenses guide the flow of e- through specimen, then e-’s are projected onto a detector and we get the image. -electro dense regions:dark grey areas, few or no e- is transmitted. -electro lucent: light grey areas, more e- transmitted because of the low density of atoms.

Differences between electron microscopy and light microscopy.

What is an antibody and who produces it in the human body?

a y shaped protein produced by b lymphocytes in response to an antigenic stimulus (bacterial/viral) which binds to a specific antigen through spatial complementarity.

What is an antigen?

any protein or non-self peptide capable of stimulating production of antibodies.

List two methods that use antibodies.

Two methods that use antibodies are immunolabelling and ELISA (enzyme linked immunosorbent assay).

What is immunolabelling and how does it work?

Immunolabelling is based on specific interactions between an antigen and an antibody. Antibodies are tagged with a detection label that allows visualization or measurement of the antigen.

What types of detection labels are used in immunolabelling?

Detection labels used in immunolabelling include: Enzymes that act on a substrate to produce a colored compound, analyzed by bright field microscopy (immunohistochemistry) or by analyzers such as spectrophotometers (ELISA) and special scanners or cameras (western blot). Fluorescent molecules, analyzed by fluorescence microscopy (immunofluorescence) or by analyzers such as flow cytometers.

What is ELISA and what is its principle?

ELISA is a method in which the detection antibody is conjugated with an enzyme. It is an enzyme (labelled antigen) antibody reaction in which the amount of antigen can be quantified by the intensity of the color generated from the enzymatic reaction.

What is the central dogma of molecular biology?

Its the statement that represents genetic information flowing in one direction, from DNA to RNA to protein, or directly from RNA to protein.

List two methods used to study nucleic acids.

PCR (Polymerase Chain Reaction). gene sequencing.

What is PCR and what is it used for?

Basically it is a method used to obtain a large number of copies of a specific gene or DNA sequence.

RT-PCR

RT-PCR works by detecting RNA through its conversion into DNA and subsequent amplification. First, RNA is extracted from the sample and converted into complementary DNA (cDNA) using the enzyme reverse transcriptase. This step is necessary because PCR can only amplify DNA. The resulting cDNA then serves as a template for PCR amplification, which proceeds through repeated cycles of denaturation, primer annealing, and elongation, producing multiple copies of the target sequence. The presence of an amplified product indicates the presence of the original RNA in the sample.

What is gene sequencing and what is it used for?

Gene sequencing is a method that determines the precise order of bases (A, T, G, C) in a DNA segment or gene. It is useful for identifying mutations, including through next generation sequencing techniques.

List two differences between nucleic acids and proteins.

Nucleic acids (DNA,RNA) are macromolecules involved in storing, transmitting, and using genetic information, whereas proteins are macromolecules composed of amino acids that perform essential life functions.

What are the primary, secondary, and tertiary structures of proteins?

The primary structure of a protein is the linear sequence of amino acids (peptide bond). The secondary structure refers to local folding patterns such as alpha helices and beta sheets(hydrogen bond). The tertiary structure is the three dimensional folding of the entire protein.

What are the main functional classes of proteins?

Major protein classes include enzymes such as helicases and polymerases, structural proteins such as lamins and nuclear matrix proteins, and carrier proteins.

What is cell culture?

Cell culture is a technique that enables the maintenance of viable cells in homogeneous populations using specially designed incubators with controlled temperature, gas composition, and humidity, in appropriate cell culture media.

Why is cell culture useful in research?

Cell culture is the simplest and most frequently used in vitro method to study living cells and their functions. It is also useful for cytotoxicity testing and for studying molecular mechanisms.

Argue why an animal model is better than a cell culture.

Animal models are superior to cell cultures because they have a higher similarity to the human genome, making them more likely to develop human or human-like diseases and allowing a more accurate study of disease mechanisms.

What are the main types of electron microscopes?

The main types of electron microscopes are Transmission Electron Microscopy (TEM) and Scanning Electron Microscopy (SEM).

What is Transmission Electron Microscopy (TEM) and what fixation methods are used?

Transmission Electron Microscopy (TEM) is an electron microscopy technique used to study the internal ultrastructure of cells and small particles. Fixation methods used in TEM include chemical fixation at room temperature and physical fixation by freezing at −190 °C.

What are the types of chemical fixation used in TEM and what are they used for?

Chemical fixation in TEM includes: Resin embedding → for cells and tissue. Negative staining → is used for small particles such as viruses and proteins.

What are the types of physical fixation used in TEM and what are they used for?

Physical fixation in TEM is performed by freezing at −190 °C and includes: High pressure freezing→ used for cells and tissue. Single particle cryo EM→ used for small particles such as viruses and proteins.

What is Scanning Electron Microscopy (SEM)?

Scanning Electron Microscopy (SEM) is a type of electron microscopy used to examine the surface morphology and three dimensional structure of specimens.

Explain the working principle of Transmission Electron Microscopy (TEM) and the meaning of electron dense and electron lucent areas.

-the e- beam is emitted continuously by a source which’s heated by a high voltage current. -it has a vacuum inside so that e- won’t collide with air molecules. -electromagnetic lenses guide the flow of e- through specimen, then e-’s are projected onto a detector and we get the image. -electro dense regions:dark grey areas, few or no e- is transmitted. -electro lucent: light grey areas, more e- transmitted because of the low density of atoms.

Differences between electron microscopy and light microscopy.

What is an antibody and who produces it in the human body?

a y shaped protein produced by b lymphocytes in response to an antigenic stimulus (bacterial/viral) which binds to a specific antigen through spatial complementarity.

What is an antigen?

any protein or non-self peptide capable of stimulating production of antibodies.

List two methods that use antibodies.

Two methods that use antibodies are immunolabelling and ELISA (enzyme linked immunosorbent assay).

What is immunolabelling and how does it work?

Immunolabelling is based on specific interactions between an antigen and an antibody. Antibodies are tagged with a detection label that allows visualization or measurement of the antigen.

What types of detection labels are used in immunolabelling?

Detection labels used in immunolabelling include: Enzymes that act on a substrate to produce a colored compound, analyzed by bright field microscopy (immunohistochemistry) or by analyzers such as spectrophotometers (ELISA) and special scanners or cameras (western blot). Fluorescent molecules, analyzed by fluorescence microscopy (immunofluorescence) or by analyzers such as flow cytometers.

What is ELISA and what is its principle?

ELISA is a method in which the detection antibody is conjugated with an enzyme. It is an enzyme (labelled antigen) antibody reaction in which the amount of antigen can be quantified by the intensity of the color generated from the enzymatic reaction.

What is the central dogma of molecular biology?

Its the statement that represents genetic information flowing in one direction, from DNA to RNA to protein, or directly from RNA to protein.

List two methods used to study nucleic acids.

PCR (Polymerase Chain Reaction). gene sequencing.

What is PCR and what is it used for?

Basically it is a method used to obtain a large number of copies of a specific gene or DNA sequence.

RT-PCR

RT-PCR works by detecting RNA through its conversion into DNA and subsequent amplification. First, RNA is extracted from the sample and converted into complementary DNA (cDNA) using the enzyme reverse transcriptase. This step is necessary because PCR can only amplify DNA. The resulting cDNA then serves as a template for PCR amplification, which proceeds through repeated cycles of denaturation, primer annealing, and elongation, producing multiple copies of the target sequence. The presence of an amplified product indicates the presence of the original RNA in the sample.

What is gene sequencing and what is it used for?

Gene sequencing is a method that determines the precise order of bases (A, T, G, C) in a DNA segment or gene. It is useful for identifying mutations, including through next generation sequencing techniques.

List two differences between nucleic acids and proteins.

Nucleic acids (DNA,RNA) are macromolecules involved in storing, transmitting, and using genetic information, whereas proteins are macromolecules composed of amino acids that perform essential life functions.

What are the primary, secondary, and tertiary structures of proteins?

The primary structure of a protein is the linear sequence of amino acids (peptide bond). The secondary structure refers to local folding patterns such as alpha helices and beta sheets(hydrogen bond). The tertiary structure is the three dimensional folding of the entire protein.

What are the main functional classes of proteins?

Major protein classes include enzymes such as helicases and polymerases, structural proteins such as lamins and nuclear matrix proteins, and carrier proteins.

What is cell culture?

Cell culture is a technique that enables the maintenance of viable cells in homogeneous populations using specially designed incubators with controlled temperature, gas composition, and humidity, in appropriate cell culture media.

Why is cell culture useful in research?

Cell culture is the simplest and most frequently used in vitro method to study living cells and their functions. It is also useful for cytotoxicity testing and for studying molecular mechanisms.

Argue why an animal model is better than a cell culture.

Animal models are superior to cell cultures because they have a higher similarity to the human genome, making them more likely to develop human or human-like diseases and allowing a more accurate study of disease mechanisms.

What are the main types of electron microscopes?

The main types of electron microscopes are Transmission Electron Microscopy (TEM) and Scanning Electron Microscopy (SEM).

What is Transmission Electron Microscopy (TEM) and what fixation methods are used?

Transmission Electron Microscopy (TEM) is an electron microscopy technique used to study the internal ultrastructure of cells and small particles. Fixation methods used in TEM include chemical fixation at room temperature and physical fixation by freezing at −190 °C.

What are the types of chemical fixation used in TEM and what are they used for?

Chemical fixation in TEM includes: Resin embedding → for cells and tissue. Negative staining → is used for small particles such as viruses and proteins.

What are the types of physical fixation used in TEM and what are they used for?

Physical fixation in TEM is performed by freezing at −190 °C and includes: High pressure freezing→ used for cells and tissue. Single particle cryo EM→ used for small particles such as viruses and proteins.

What is Scanning Electron Microscopy (SEM)?

Scanning Electron Microscopy (SEM) is a type of electron microscopy used to examine the surface morphology and three dimensional structure of specimens.

What is de novo formation of peroxisomes?

Formation of a precursor vesicle in the ER followed by loading of peroxisomal proteins.

How are new mitochondria formed?

New mitochondria are formed by fission of pre-existing mitochondria.

What role do small GTP-binding proteins (GTPases) play during translation?

Small G proteins control all stages of translation.

Compare prokaryotic and eukaryotic cells, emphasizing DNA organization.

Prokaryotic DNA is usually circular and not associated with histones. Eukaryotic DNA is linear and associated with histone proteins.

What are gap junctions and what is their functional significance?

Gap junctions are communication junctions that allow passage of ions and small molecules between adjacent cells. They are present in intercalated discs.

Why do lysosomes maintain an acidic internal pH?

Lysosomes maintain an acidic pH because acid hydrolases require an acidic environment to function.

Describe the structure and functions of the cytoskeleton.

The cytoskeleton is a network of actin filaments, intermediate filaments, and microtubules that maintains cell shape, provides mechanical support, enables cell movement, participates in cell division, supports membrane specializations, and mediates intracellular transport.

What is the significance of promoter methylation in gene regulation?

Promoter methylation causes inactivation of gene transcription.

What is exocytosis and what role does it play in secretion?

Exocytosis is the final step of the secretory pathway involving release of vesicle contents outside the cell.

Explain how extracellular signals are transmitted into the cell.

Signaling molecules bind to receptors, inducing conformational changes that activate intracellular signaling pathways and generate a cellular response.

Describe the barrier function of the plasma membrane.

The plasma membrane forms a selective barrier through its hydrophobic phospholipid bilayer, which separates the intracellular and extracellular environments. It allows some molecules to pass while restricting the movement of polar, charged, and large molecules. Transport proteins regulate the passage of substances across the membrane.

What is facilitated transport and how is it mediated by carrier proteins?

Facilitated transport is passive transport through carrier proteins or channels.

How are newly synthesized proteins targeted and transferred to the rough endoplasmic reticulum?

Signal recognition particle (SRP) binds N-terminal signal sequence and directs proteins to the rough ER.

What is a cell-cycle checkpoint and why is it important?

A cell-cycle checkpoint is a regulatory point where progression can continue or stop.

Describe the structure and functions of the nuclear envelope.

Formed by inner and outer nuclear membrane + perinuclear space (nuclear envelope lumen). Double membrane surrounding nucleus. Only present in interphase. Maintains nuclear integrity.

Explain the detoxification functions of the smooth endoplasmic reticulum.

Converts water-insoluble substances into water-soluble compounds for excretion.

Discuss the structure and functions of cadherins and their role in cell adhesion.

Cadherins are cell adhesion proteins important for intercellular junctions.

What is the clinical significance of the mitochondrial genome?

Maternal transmission of mitochondrial DNA mutations that can cause severe diseases.

Compare primary and motile cilia and discuss their functions.

Primary cilium is involved in detection and response to extracellular signals. Mobile cilium has an axoneme composed of 9 peripheral microtubule doublets and 2 central microtubules and is involved in movement.

Explain how antibodies can promote phagocytosis by macrophages.

Macrophages recognize antibody-coated pathogens through Fc receptors.

What mechanisms are responsible for the two-dimensional fluidity of the cell membrane?

Lateral and rotational movement of membrane lipids.

Discuss the functions of the nucleolus.

Ribosome biogenesis and assembly of signal recognition particles.

How do lysosomes participate in cell signaling?

Termination of signaling by degradation of ligands.

What are lysosomal storage diseases and how do they develop?

Accumulation of undigested substrates due to lysosomal enzyme deficiency.

Explain the relationship between the genome and the proteome and why the proteome is more complex.

Proteome is the complete set of proteins expressed by a cell. The proteome is more complex than the genome because post-transcriptional and post-translational modifications create more proteins than genes.