Biotechniques: Biosafety Overview

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Questions and Answers

What is the main purpose of an objective lens in a microscope?

To stabilize the microscope

To focus light on the detector

To provide illumination for the specimen

To magnify the specimen (correct)

Which total magnification is achieved when using a high power objective lens with a power of 40X and an ocular lens of 10X?

100X

1000X

40X

400X (correct)

When is immersion oil necessary in microscopy?

When using a stereomicroscope

When examining live specimens

When using the oil immersion lens (correct)

When using low power magnification

What does the field of view in a microscope refer to?

The area of the slide seen through the eyepiece Signup and view all the answers

What type of microscope is specifically suitable for the observation of large specimen surfaces and 3D information?

Stereomicroscope Signup and view all the answers

Which of the following statements about lenses in microscopy is true?

High power objectives typically use oil immersion. Signup and view all the answers

What is the primary function of a digital camera when used with a microscope?

To capture images of the specimen Signup and view all the answers

What distinguishes interchromosomal insertion from intrachromosomal insertion?

Interchromosomal insertion involves a different chromosome. Signup and view all the answers

Which of the following describes gene amplification?

An increase in the number of tandem copies of a locus. Signup and view all the answers

What contributes to the identification of mutation hotspots in the genome?

Areas with highly repetitive sequences that attract mutagens. Signup and view all the answers

How do mitochondrial DNA mutations affect cellular function?

They disrupt cellular energy generation efficiency. Signup and view all the answers

What is a translocation in genetic terms?

The reunion of broken pieces from two different chromosomes. Signup and view all the answers

What constitutes a molecule?

Atoms bonded together, which can be the same or different Signup and view all the answers

Which of the following elements make up over 90% of the human body?

Carbon, nitrogen, oxygen, hydrogen Signup and view all the answers

What is the main characteristic of ionic bonds?

The attraction between positively and negatively charged ions Signup and view all the answers

How do double covalent bonds differ from single covalent bonds?

They share two pairs of electrons instead of one Signup and view all the answers

What defines a polar molecule, such as water?

It has different electrical poles within the molecule Signup and view all the answers

Which statement about covalent bonding is true?

Electrons are shared between atoms to fill their valence shells Signup and view all the answers

Which of the following best describes the role of buffers in biological systems?

Buffers help in neutralizing acids without changing pH radically Signup and view all the answers

What is an isotope?

An atom with the same number of protons but different neutrons Signup and view all the answers

What primarily makes organic molecules different from other types of molecules?

Organic molecules contain hydrogen and are primarily derived from biological sources Signup and view all the answers

What is the advantage of artificial gene synthesis compared to traditional methods?

It allows for the creation of completely synthetic DNA molecules. Signup and view all the answers

What is the function of a microarray in genetic research?

It detects the expression of thousands of genes simultaneously. Signup and view all the answers

Which factor can lead to spontaneous mutations?

Errors during DNA replication. Signup and view all the answers

What are germline mutations?

Mutations that occur in gametes. Signup and view all the answers

Which of the following statements about mutations is correct?

Somatic mutations occur in non-reproductive cells. Signup and view all the answers

What is the primary cause of induced mutations?

Exposure to environmental factors. Signup and view all the answers

What role do chemical mutagens play in DNA?

They induce point mutations. Signup and view all the answers

How does the principle of DNA microarrays work?

It relies on complementary sequences binding to each other. Signup and view all the answers

In the context of DNA, what are purine and pyrimidine bases known for?

They contribute to the chemical stability of DNA. Signup and view all the answers

What is the significance of clustering expression profiles in research?

It defines subtypes of breast cancer cell lines. Signup and view all the answers

What is the primary purpose of DNA cloning?

To reproduce inserted DNA with a vector Signup and view all the answers

Which of the following best describes plasmids?

Circular, self-replicating, double-stranded DNA Signup and view all the answers

What technique uses DNA polymerase to amplify specific DNA sequences?

Polymerase Chain Reaction (PCR) Signup and view all the answers

Which of the following vectors is often used for cloning in E. coli?

E. coli plasmid vectors Signup and view all the answers

What is not a common type of molecular hybridization technique?

PCR amplification Signup and view all the answers

Which method is used for introducing mutations into DNA?

Random mutagenesis Signup and view all the answers

What are the types of blotting used in molecular biology for different purposes?

Southern, Northern, and Western blots Signup and view all the answers

What is the primary role of a vector in DNA cloning?

To facilitate the replication of inserted DNA Signup and view all the answers

Which of the following statements is false regarding CRISPR/Cas9?

It relies on DNA polymerase for DNA amplification. Signup and view all the answers

Which of the following methods is not a function of gel electrophoresis?

Enhancing plasmid replication Signup and view all the answers

Which of the following best describes the structure of smooth muscle fibers?

Cylindrical with pointed ends and uninucleated Signup and view all the answers

What is a distinguishing feature of cardiac muscle tissue?

Intercalated disks connect fibers Signup and view all the answers

Which of the following functions is NOT performed by skeletal muscles?

Pumping blood Signup and view all the answers

How do skeletal muscle fibers differ from smooth muscle fibers?

Skeletal muscle fibers are striated and multinucleated Signup and view all the answers

What role do the neuromuscular junctions play in muscle contraction?

They initiate the contraction of muscle fibers Signup and view all the answers

What is one key characteristic of the sliding filament model of muscle contraction?

Actin and myosin filaments slide past each other Signup and view all the answers

Which type of muscle tissue displays rhythmic contractions without nervous stimulation?

Cardiac muscle Signup and view all the answers

What is the term for the muscle that is contracting during movement?

Agonist Signup and view all the answers

Which of the following is NOT a component of a muscle fiber?

Nucleus Signup and view all the answers

What type of myofilament is composed of myosin?

Thick Myofilaments Signup and view all the answers

Which structure penetrates the muscle fibers and comes close to the sarcoplasmic reticulum?

T-tubules Signup and view all the answers

What is the function of myoglobin in muscle fibers?

Binding oxygen Signup and view all the answers

What would happen if both the agonist and antagonist muscles contract simultaneously?

No movement occurs Signup and view all the answers

Which part of a muscle fiber is responsible for calcium storage?

Sarcoplasmic reticulum Signup and view all the answers

Where are myofibrils located within a muscle fiber?

Embedded in sarcoplasm Signup and view all the answers

What provides energy for muscle contraction?

Glycogen Signup and view all the answers

What is the role of myoglobin in muscle fibers?

It contains oxygen for energy production during muscle contraction. Signup and view all the answers

What is the structure that separates sarcomeres in muscle fibers?

Z line Signup and view all the answers

What happens to the I band during the contraction of a muscle fiber?

It shortens. Signup and view all the answers

Which of the following correctly describes thick myofilaments?

They consist of the protein myosin. Signup and view all the answers

What is the function of the sarcoplasmic reticulum in muscle fibers?

To store calcium ions necessary for contraction. Signup and view all the answers

Which statement is true regarding the sliding filament model of muscle contraction?

The thin filaments slide past the thick filaments. Signup and view all the answers

What primary component gives rise to muscle striations?

The arrangement of myofilaments. Signup and view all the answers

What structure extends into the muscle fiber and conducts impulses to trigger calcium release?

T tubule Signup and view all the answers

Which region of the sarcomere contains only thick myofilaments?

H band Signup and view all the answers

What mechanism describes the continuous sliding action of myosin and actin filaments during muscle contraction?

Ratchet mechanism Signup and view all the answers

Which of the following sources of energy for muscle contraction is stored directly in muscle cells?

Creatine phosphate Signup and view all the answers

Which pathway for ATP production in muscle cells requires oxygen?

Cellular respiration Signup and view all the answers

What role do calcium ions (Ca2+) play in muscle contraction?

Trigger the contraction mechanism Signup and view all the answers

As the duration of exercise increases, which source of energy is predominantly utilized by muscles?

Fatty acids from blood Signup and view all the answers

What action occurs when acetylcholine (ACh) binds to receptors in the sarcolemma?

Electric signals are generated and spread across the sarcolemma. Signup and view all the answers

What is the primary role of calcium ions (Ca2+) in muscle contraction?

To bind to troponin and expose myosin-binding sites. Signup and view all the answers

What sequence of events occurs first in the sliding filament theory of muscle contraction?

Myosin heads form cross-bridges with actin. Signup and view all the answers

What happens after the power stroke in muscle contraction?

ADP and P are released, causing the myosin heads to bend. Signup and view all the answers

Which component is crucial for the removal of cross-bridges during muscle contraction?

ATP Signup and view all the answers

What is found in the synaptic vesicles at an axon terminal?

Acetylcholine Signup and view all the answers

Which area describes the junction between a motor neuron and a muscle fiber?

Neuromuscular junction Signup and view all the answers

How does tropomyosin affect muscle contraction?

It covers myosin-binding sites on actin. Signup and view all the answers

What role does the axon play in muscle fiber contraction?

It stimulates muscle contraction. Signup and view all the answers

What occurs when the nerve signal reaches an axon terminal?

Acetylcholine is released into the synaptic cleft. Signup and view all the answers

Study Notes

Biotechniques (BMS 34010A)

Course offered during Fall semester 2023-2024
Instructor: Dr. Tania Tahtouh
Email: [email protected]

Basic Principles: Biosafety in the Laboratory

Laboratory settings present potential hazards.
Safety procedures protect personnel and equipment.
Disposal of contaminated materials/chemicals follows strict protocols.

Potential Laboratory Hazards

Corrosive chemicals, sharp tools/glass, and open flames pose risks.
Bunsen burners require extreme caution.
Infectious organisms also pose hazards, classified into biosafety levels (BSL 1-4).
Most undergrad labs use BSL 1 organisms.

Standard Practices in the Laboratory

Lab coats are essential for protection against contamination.
Lab coats should be long and not restrict movement.
Lab coats are not chemical protection suits.
Gloves should not touch surfaces outside the lab.
Eating, drinking, chewing gum, or pipetting by mouth are forbidden in the lab.
No makeup or contact lenses adjustments in the lab.
Work area must be clean with only necessary materials.
Cell phones, bags, and other items should be stored away from workbench.
Avoid leaving active experiments unattended.
Properly disinfect the workbench before and after each experiment.
Maintain clean hands and use correct hand washing techniques.
Unauthorized experiments are forbidden.
Long hair must be tied up, and loose clothes must be secured when working with open flames.
Safety glasses or face shields required when working with UV light or chemicals.
Closed-toe shoes are mandatory to avoid chemical spills and sharp objects.
Know location of safety equipment: eyewash, chemical shower, first-aid kit, and fire extinguisher.
Follow chemical hygiene plans and use fume hoods/biosafety cabinets for chemical handling.
Report spills, accidents, or injuries immediately.

Biohazard Bin

Biohazardous waste goes in appropriately labeled bins/bags.
Non-reusable items with contact to infectious material, body fluids, or animal tissue.
Handled gloves must also be disposed of.
Items can be autoclaved before disposal.

Sharps Containers & Trash Cans

Sharps containers for broken glass, needles, used scalpels, glass pipettes, and other sharp objects.
Non-contaminated items (paper, etc.) go in regular trash cans.

Reusable Materials

Materials needing sterilization: autoclave after use (e.g., culture tubes and instruments).
Materials not needing sterilization: wash in sink after use (e.g., dissection tools and glassware).

General Rules for Handling Chemicals

Keep containers closed.
Never handle wrong or unmarked reagents.
Avoid carrying bottles by the neck or against the body.
Labels should face up when pouring.
Only place indicated chemical into bottle.
Handle concentrated acids with caution (add acid to water and stir continuously).
Disposal of some chemicals requires special procedures.

The Importance of Hand Washing

Hand washing is crucial in labs, especially microbiology.
Hands can come into contact with infectious agents, chemicals, stains, and other hazardous materials.
Wash hands before, after, and whenever contact with potential hazards occurs.

Steps for Correct Hand Washing Technique

Remove all jewelry.
Wet hands and apply soap.
Rub hands together to make a lather.
Scrub for 20 seconds (e.g., "Happy Birthday" twice).
Rinse and dry hands with a clean towel/air dry.

Metric Systems

The SI system (International System of Units) is the standard used by scientists.
The United States is the only industrialized nation to continue using the English system.
SI system is based on the number 10.
The SI system includes measurement units for length, mass, volume, temperature, and time.

Microscopy: Types and Principles

Biological specimens often require microscopic visualization.
Various types of microscopes exist for different applications.
Types of microscopes include Light (compound, binocular, phase contrast, fluorescent, confocal) and Electron (transmission, scanning).
Learning Outcomes: Recognize principles/uses of different microscopes, parts of a compound light microscope, total magnification, microscope rules of use, focus methods, field of view, longitudinal/cross sections, and resolution.
Light Microscopes: Simplest consists of a single glass lens. -Specimen prep minimal. -Focusing by moving specimen relative to lens.
Compound Light Microscopes: Multiple lenses (condenser, objective, eyepiece).
Parts of Compound Light Microscope
- Light source (lamp).
- Condenser.
- Objectives.
- Eyepiece.
- Stage & Clips.
- Diaphragm
- Coarse & Fine Focus Knobs.

-Lens types and Magnification.

Field of view (at low and high power).
Longitudinal & cross sections.
Resolution.
Scanning and Transmission Electronic Microscopes: Greater magnification to view smaller objects
Stereomicroscope: Used to observe large specimens' surfaces in 3-D.
Phase contrast microscopy: Improves contrast for transparent and colorless specimens.
Fluorescent microscopy: High contrast for specific labeling of cellular components.
Fluorescents and stains (RFP, GFP, and DAPI).
Immunofluorescence: Using antibodies labeled with fluorescent dyes.
Confocal microscopy: Produces optical sections of thick specimens.
Microscope use rules outlined in slide deck

DNA Cloning Overview

Inserting the target DNA into the plasmid vector.

Cut and Paste DNA: Plasmids

Circular
Self-replicating.
- Host cell/chromosome separate.

Cut and Paste DNA: Euk expression vectors

-Eukaryotic DNA containing virus restriction sites and/or terminal repeats.

Cut and Paste DNA: Restriction

Restriction Sites: Specific 4-8 bp.
Type II Restriction Enzymes: Highly-specific, blunt, or sticky ends.

Cut and Paste DNA: Restriction (Inserting DNA sample into plasmid):

Enzymes cut DNA at restriction sites, and ligase joins the fragments.

DNA Transfer into Cells (Transformation, Transduction, Transfection)

Transformation (prokaryotic) - Non-viral method
Transduction (prokaryotic/eukaryotic) - Viral method
Transfection (eukaryotic) - Non-viral method

Chromosome Integration

Integrase splices viral DNA into the cellular chromosome.

Cellular Screening

Vectors derived from natural plasmids; genetically modified for convenient use, some more advanced than others in structure .

DNA Extraction

Lysis
Precipitation
Purification
Elution

Extraction of Plasmids

Separation of plasmid/chromosomal DNA through differential denaturation and neutralization.

DNA Cloning Overview

Gene amplification and digestion/ligation.
Transformation & plasmid isolation/sequencing.

Crispr/Cas9

A genome editing technique in bacteria.
Creation of specific double-strand breaks at the target locus.
Types: NHEJ and HR

DNA Synthesis

Artificial gene synthesis not requiring DNA template.

DNA Array (Microarray)

Tool for detecting gene expression.

Mutations and Causes

Spontaneous Mutations: Errors in replication or chemical instability of DNA bases.
Induced Mutations: Exposure to environmental factors.

Main Types of Mutations

Germline: Inherited, in gametes.
Somatic: In other body cells.
Point mutations: Substitutions, insertions, or deletions of single bases.
Chromosomal mutations: Deletions. Duplications. Inversions, insertions, translocations.
Copy Number Variation (CNV): Changes in the number of tandem copies of a locus.

Point Mutations

Missense: Different amino acid.
Nonsense: Premature stop codon.
Synonymous: Same amino acid.
Neutral: No effect.

Point Mutations: Categorization

Loss-of-function: Decreased/absent gene product.
Gain-of-function: Increased gene product or new activity

Chromosomal Mutations

Deletion: Loss of chromosome region.
Duplication: Repetition of chromosome region.
Inversion: Flipping and reinserting a chromosome region.
Insertion: Moving a chromosome region to another.
Translocation: Rearrangement of chromosome regions.

Copy Number Variation (CNV)

Gene amplification: Increasing tandem copies of a locus.
Expanding trinucleotide repeat: Expanding repeated sequences.

Mutation Hotspots

Regions with higher recombination rates or accessibility to mutagens.
Repetitive sequences are often hotspots.

Mitochondrial DNA Mutations

Inherited changes can cause growth/development/function problems.
mtDNA mutations affect mitochondria's energy generation capacity.
References: Provide links to relevant articles & resources.

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Description

This quiz covers the essential biosafety principles in laboratory settings, focusing on the identification of potential hazards and standard practices to ensure safety. It is designed for students enrolled in the Biotechniques course (BMS 34010A) for the Fall semester of 2023-2024.