Scientific Research Final

What is the primary use of phalloidin staining in cell biology?

To visualize filamentous actin (F-actin)

Phalloidin binds specifically to which cellular structure?

F-actin (filamentous actin)

Why is phalloidin commonly conjugated with fluorescent dyes for microscopy?

To visualize F-actin under a fluorescence microscope

Phalloidin binding to F-actin is generally considered:

Irreversible and strong

Why is permeabilization necessary in the phalloidin staining procedure?

To allow phalloidin to enter the cells and bind intracellular F-actin

Which reagent is commonly used to permeabilize cells before phalloidin staining?

Triton X-100

What effect does phalloidin have on actin filaments?

It stabilizes and prevents depolymerization

What is the first step in a typical phalloidin staining protocol for cells?

Fixation of cells

Which fixative is most used in phalloidin staining to preserve actin filaments?

Formaldehyde (paraformaldehyde)

Phalloidin conjugated to a fluorophore is typically incubated with the sample for:

20-60 minutes

What is the purpose of washing the cells after phalloidin incubation?

To remove unbound phalloidin and reduce background fluorescence

After phalloidin staining, the sample is usually mounted with:

Mounting medium containing an anti-fade reagent

What is the primary purpose of cell culture in biological research?

To grow cells outside their natural environment for experimental purposes

Which of the following is a common basal medium for mammalian cell culture?

DMEM

Which of the following is essential for maintaining cell growth in culture?

All of the above (sterile conditions, appropriate pH & temperature, nutrients & growth factors)

Trypsin is used in cell culture primarily for:

Detaching adherent cells from the culture vessel

Contamination in cell culture is most caused by:

All of the above (viruses, fungi, bacteria)

Fetal bovine serum (FBS) is added to cell culture media to:

Provide nutrients, hormones, and growth factors

A monolayer culture refers to:

Which method is commonly used to check cell viability?

Trypan blue exclusion assay using automatic counter

Which of the following is a common feature of immortalized cell lines?

Ability to divide indefinitely

Which condition is critical for preventing bacterial contamination in cell culture?

All of the above (working in a biosafety cabinet, using autoclaved instruments and media, regularly disinfecting surfaces)

What is the function of HEPES in cell culture media?

Maintains pH stability

Which method is used to freeze mammalian cells for long-term storage?

Gradual freezing with cryoprotectants like DMSO

In a culture flask, cells begin to grow and cover the entire surface. This phase is called:

Confluence

What is the primary purpose of cell culture media?

To provide nutrients, growth factors, and an appropriate environment for cells

The role of glucose in cell culture media is to:

Act as a carbon and energy source

Which of the following steps is essential before using media for cell culture?

Sterilization through filtration or autoclaving

Antibiotics like penicillin-streptomycin are added to media to:

Prevent bacterial contamination

L-glutamine is added to cell culture media because it is:

An essential amino acid for protein synthesis

When preparing media, why is sterile filtration often preferred over autoclaving for heat-sensitive components?

It prevents degradation of vitamins, growth factors, and amino acids

Phenol red in culture media acts as:

A pH indicator

Which of the following practices ensures media sterility after preparation?

All of the above (working in a laminar flow hood, using sterile bottles and pipettes, avoiding repeated exposure to air)

Which of the following structures is NOT found in prokaryotic cells?

Nucleus

What is the primary difference between prokaryotic and eukaryotic cells?

Prokaryotic cells lack a nucleus, eukaryotic cells have a nucleus

Which of the following is a common feature of prokaryotic cells?

Circular DNA

In prokaryotic cells, where is the genetic material primarily located?

Nucleoid region

Which of the following components is found in the cell wall of most prokaryotes?

Peptidoglycan

What is the function of the flagella in prokaryotic cells?

Movement

Which of the following processes is typical for prokaryotic reproduction?

Binary fission

What term describes the hair-like structures used by some prokaryotes for attachment to surfaces?

Pili (or fimbriae)

Which of the following best describes the size of prokaryotic cells compared to eukaryotic cells?

Smaller

Prokaryotic ribosomes are classified as:

70S

Which of these groups are prokaryotes?

Archaea and Bacteria

In prokaryotes, plasmids are:

Circular DNA molecules separate from chromosomal DNA

Which organelle is known as the “control center” of the eukaryotic cell

Nucleus

Which of the following structures is found in eukaryotic cells but NOT in prokaryotic cells?

Mitochondria

What type of DNA does eukaryotic cells typically have?

Linear DNA wrapped around histones

Which organelle is responsible for energy production in eukaryotic cells?

Mitochondrion

Which of the following is a function of the Golgi apparatus?

Packaging and transporting proteins

Eukaryotic ribosomes are classified as:

80S

Which organelle contains enzymes to break down waste and cellular debris?

Lysosome

Which of the following organelles is responsible for photosynthesis in plant cells?

Chloroplast

The cytoskeleton in eukaryotic cells is important for:

Maintaining cell shape and movement

Which of the following is NOT a membrane-bound organelle in eukaryotic cells?

Ribosome

Which part of the eukaryotic cell is involved in synthesizing lipids and detoxifying chemicals?

Smooth Endoplasmic Reticulum

During which phase of the cell cycle does DNA replication occur in eukaryotic cells?

S Phase

Which organelle modifies proteins and packages them into vesicles for transport?

Golgi Apparatus

What type of eukaryotic cells lacks a cell wall?

Animal cells

What is the primary function of mitochondria in eukaryotic cells?

ATP Production

Which organelle helps in detoxifying harmful substances and contains catalase enzyme?

Peroxisome

Which cytoskeletal element is primarily responsible for cell division by forming the mitotic spindle?

Microtubules

Which eukaryotic organelle contains its own DNA and is believed to have originated from a symbiotic relationship with bacteria?

Mitochondria

What is the key feature that allows Sanger sequencing to terminate DNA extension?

Use of dideoxynucleotides (ddNTPs)

Why do dideoxynucleotides cause chain termination?

They lack a 3′ hydroxyl group

In modern Sanger sequencing, fluorescent dyes are typically attached to:

ddNTPs (dideoxynucleotides)

What is the first step of the Sanger sequencing workflow?

DNA denaturation

In Sanger sequencing electropherograms, a peak with two overlapping colors typically indicates:

Heterozygosity at that nucleotide position

Which enzyme is used in Sanger sequencing?

DNA polymerase I (Klenow fragment) in classical methods

Capillary electrophoresis separates fragments based on:

Fragment size/length

Typical read length for Sanger sequencing is:

500–1000 bp

Sanger sequencing is best suited for:

Small targeted regions (e.g., single gene mutations)

In dye‑terminator sequencing, each of the four ddNTPs

Has its own unique fluorescent label

The template strand in Sanger sequencing must be:

Single‑stranded DNA or denatured dsDNA

If the primer anneals at the wrong location, the most likely issue is:

Low annealing temperature

The final output of Sanger sequencing is a:

Chromatogram with colored peaks

Which component is essential for initiating DNA synthesis in Sanger sequencing

A single, sequence‑specific primer

In capillary electrophoresis, DNA fragments move toward which electrode

Anode

Which of the following is TRUE for Sanger sequencing compared to whole genome sequencing?

Sanger produces longer reads

A double peak at a single position suggests:

Mixed template (e.g., heterozygote)

 A sequencing reaction contains four separate tubes in classical Sanger sequencing. What does each tube contain?

Only one type of ddNTP

A sequencing reaction yields very short fragments only. What is a common cause?

Only one type of ddNTP

Nanopore sequencing is particularly useful for:

Detecting structural variants and large genomic rearrangements

Which template type is MOST problematic for Sanger sequencing?

Mixed plasmids

Which step in Sanger sequencing is responsible for separating DNA fragments by length?

Capillary electrophoresis

Why is only one primer used in Sanger sequencing?

To prevent exponential amplification

If the sequencing machine detects overlapping fluorescent signals, it may miscall a base due to:

Incomplete separation of fragments

What is the basic principle of nanopore sequencing?

Measurement of changes in ionic current as nucleic acids pass through a nanopore

Which company developed the MinION device for nanopore sequencing?

Oxford Nanopore Technologies

What is a major advantage of nanopore sequencing compared to second-generation sequencing?

Generates long reads in real time

What type of molecules can nanopore sequencing analyze?

DNA and RNA

What controls the speed of DNA translocation through the nanopore

Motor proteins

Which signal is measured in nanopore sequencing?

Ionic current disruption

Why must DNA damage be repaired?

DNA damage can lead to cancer

 A permanent change in the DNA sequence is called:

Mutation

Which inherited disease mentioned in the presentation is caused by DNA mutation?

Sickle Cell Anemia

Which of the following is NOT a cause of DNA damage?

Ribosomes

 Approximately how many DNA damages can occur per cell per day?

1 million

DNA damage can be broadly classified into:

Single base changes and structural changes

Deamination of cytosine converts it into:

Uracil