Laboratory methods

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Questions and Answers

What does the equation 'Genes + Environment = Modifiable Outcome of Physiome' represent in the context of phenomics?

The impact of drug discovery on genetic material.

The complexity of genetic sequencing.

The necessity of high-resolution microscopy.

The relationship between genetics and environmental interaction. (correct)

Which of the following omics approaches focuses on understanding the physiological relevance within an intact biological milieu?

Phenomics (correct)

Genomics

Metabolomics

Cellomics

Which type of microscope uses visible light and lenses, serving as a foundational tool in biology?

Optical microscope (correct)

Confocal microscope

Fluorescence microscope

Electron microscope

What improvement has modern technology provided to optical microscopy?

Enhanced image quality and resolution. Signup and view all the answers

Which omics field allows for drug discovery without prior knowledge of molecular targets?

Physiomics Signup and view all the answers

What is the primary goal of studying omics in drug discovery?

To increase physiological relevance of bioassays. Signup and view all the answers

When were the first basic optical microscopes developed?

17th century Signup and view all the answers

Which of the following best exemplifies biological complexity within the context of omics?

Analyzing interconnected omics fields. Signup and view all the answers

What is the role of antibodies in the immune system?

Bind to antigens and neutralize pathogens Signup and view all the answers

What do immunofluorescence techniques utilize to identify specific target molecules?

Fluorescent probes and antibodies Signup and view all the answers

Which of the following describes an antigen?

A molecular structure targeted by antibodies Signup and view all the answers

What is necessary for cells before they are examined under a microscope?

They need to be prepared through fixation, staining, and sectioning Signup and view all the answers

What characteristic of antibodies allows them to specifically bind to antigens?

Their structure and variable regions Signup and view all the answers

What is the primary function of fluorochromes in immunofluorescence?

Produce visible light for imaging Signup and view all the answers

Which statement about antibodies is correct?

They are Y-shaped proteins produced by B lymphocytes. Signup and view all the answers

How do antibodies contribute to the neutralization of viruses?

By binding to proteins on the surface of viruses Signup and view all the answers

What is a characteristic feature of monoclonal antibodies?

They are produced by identical immune cells. Signup and view all the answers

What does the term 'monovalent affinity' refer to in the context of monoclonal antibodies?

Binding to a single specific epitope. Signup and view all the answers

Which method involves labeling antibody molecules with a fluorescent dye directly?

Primary immunofluorescence. Signup and view all the answers

In secondary immunofluorescence, what role does the secondary antibody play?

It binds to the primary antibody to enable detection. Signup and view all the answers

What advantage does fluorescent microscopy provide in cellular imaging?

It can image multiple stained molecules simultaneously. Signup and view all the answers

What is the purpose of using fluorescent filters in fluorescent microscopy?

To isolate specific wavelengths of emitted light. Signup and view all the answers

How are monoclonal antibodies primarily produced in the laboratory?

By injecting a foreign protein into an animal host. Signup and view all the answers

What is an epitope?

The site on the antigen recognized by an antibody. Signup and view all the answers

What is the isoelectric point of a protein?

The pH at which the net charge of the protein is zero Signup and view all the answers

What is the purpose of Western blotting?

To detect separated proteins using antibodies Signup and view all the answers

How is enzyme kinetics primarily measured?

By determining the rate of product formation with a spectrophotometer Signup and view all the answers

What shape does the plot of v versus substrate concentration [S] typically take?

Hyperbolic Signup and view all the answers

What happens to the reaction velocity when substrate concentration [S] is low?

Doubling the concentration will double the reaction velocity Signup and view all the answers

What is saturation in enzyme kinetics?

When all enzyme sites are filled and active Signup and view all the answers

What limits the maximum velocity (Vmax) in enzyme kinetics?

The number of enzyme molecules available Signup and view all the answers

What happens as substrate concentration [S] approaches infinity?

Reaction velocity approaches the maximum velocity (Vmax) Signup and view all the answers

What key measurement does Vmax provide for an enzyme-catalyzed reaction?

The potential maximum rate of the reaction Signup and view all the answers

Which statement accurately describes the role of Km in enzyme kinetics?

Higher Km values indicate a higher substrate concentration required for enzyme action Signup and view all the answers

What is the primary benefit of using the double-reciprocal plot in enzyme kinetics?

It simplifies the determination of Vmax and Km Signup and view all the answers

What is the function of restriction endonucleases?

To cleave DNA at specific recognition sequences Signup and view all the answers

How do shorter DNA fragments behave in gel electrophoresis compared to longer fragments?

They migrate more rapidly towards the positive electrode Signup and view all the answers

What is the purpose of using a nucleic acid probe in Southern blotting?

To identify a specific DNA sequence via base-pairing Signup and view all the answers

During Southern blotting, what is done to the DNA before applying the nucleic acid probe?

It is denatured for easier binding Signup and view all the answers

Study Notes

Phenomics: The Next Frontier

Phenomics integrates genomics and environmental influence to predict an organism's physiological outcome.
The "physiome" refers to the complete set of physiological processes within a living organism.

Omics: A Scalar Approach to Life

Omics approaches involve investigating the complete sets of different types of molecules and biological structures.
These range from genomics (DNA) to transcriptomics (RNA) and proteomics (proteins) to metabolomics (metabolites) and cellomics (cells).
Phenomics sits at the top, integrating all these levels to study the complete physiological function.
This approach aids in understanding biological complexities and offers a pathway for personalized medicine.

Omics in Drug Discovery

Phenomics and physiomics provide an alternative approach to traditional drug discovery by studying entire physiological systems.
This approach utilizes bioassays within an intact physiological milieu, avoiding the need for prior knowledge of molecular targets.
Studying phenotypes and physiomies gives insight into drug effect on complete biological systems, enhancing drug efficacy and precision.

Microscopy: Seeing cells

Microscopy is a fundamental tool in cell biology, offering diverse techniques to see and analyze living cells.
The optical microscope, using visible light and lenses, was the first, while advancements have led to various high resolution imaging methods.

Types of Microscopy

Different light microscopy techniques exploit various properties of light to visualize cells, including fluorescence and confocal microscopy.
Electron microscopy offers even higher resolution via electron beams, enabling the visualization of intracellular structures and even molecules.

Cell Preparation for Microscopy

Cells often require preparation before microscopy, which can include:
- Fixation: Stabilizing cells to preserve structure.
- Staining: Employing dyes to highlight specific cellular components.
- Sectioning: Thinly slicing cells for viewing internal structures.

Immunofluorescence: Staining with Antibodies

Immunofluorescence uses fluorescent probes combined with antibodies to locate specific molecules within cells.
Antibodies, known as immunoglobulins, are produced by immune cells, targeting specific structures called antigens.
This technique allows researchers to visualize and analyze the location and abundance of specific molecules within cells.

Antibodies: Defense Proteins

Antibodies are produced by white blood cells called B lymphocytes in response to the presence of antigens.
They bind to and neutralize pathogens (bacteria, viruses) or mark them for destruction by immune cells.
Antibodies are Y-shaped proteins with a constant region (C), common to the antibody type, and variable regions (V) that bind distinct antigens.

Antigens: Targets of Antibodies

Antigens are molecular structures that are specifically recognized and bound by antibodies.
Each antibody binds to a specific epitope, a part of the antigen, allowing the immune system to identify and respond to specific threats.
Antibodies can be engineered to target specific antigens for scientific and medical purposes.

Monoclonal Antibodies: Mass-Produced Specificity

Monoclonal antibodies (mAbs) are laboratory-produced antibodies that bind to the same epitope, enabling high specificity and reproducibility.
They are generated by cloning a single immune cell that produces a specific antibody, allowing for mass production for research and therapeutic applications.

Immunofluorescence: Direct vs. Indirect

Direct Immunofluorescence: Fluorescent dyes are directly attached to primary antibodies that specifically bind to the target molecule.
Indirect Immunofluorescence: Unlabeled primary antibodies bind to the target, followed by labeled secondary antibodies that bind to the primary antibodies, enhancing signal.

Fluorescent Microscopy: Imaging Specific Signals

Fluorescent microscopy uses filters to detect specific wavelengths of light emitted by fluorescent probes, allowing distinct signals to be visualized.
Different combinations of probes and filters enable the simultaneous imaging of multiple cellular structures and molecules.

Two-Dimensional Gel Electrophoresis: Separating Proteins

2D SDS-PAGE combines two techniques to separate proteins based on both size and charge:
- Isoelectric focusing: Separating proteins based on their isoelectric point (the pH where the net charge is zero).
- SDS-PAGE: Separating proteins based on molecular size using sodium dodecyl sulfate (SDS) and gel electrophoresis.

Western Blotting: Detecting Specific Proteins

Western blotting identifies specific proteins within a complex mixture:
- Proteins are first separated by size using SDS-PAGE.
- Separated proteins are transferred to a membrane (nitrocellulose or nylon) using an electric current.
- Specific proteins are then detected using labeled antibodies, which bind to their corresponding antigens.

Studying Enzymes:

Enzyme kinetics studies the rate of enzyme-catalyzed reactions, which is influenced by enzyme, substrate, and environmental factors.
Spectrophotometers measure the absorbance of light by solutions, allowing the progress of reactions to be monitored by changes in reactant or product concentration.
The dependence of reaction velocity (v) on substrate concentration ([S]) is often described by a hyperbolic curve.
Saturation: At high substrate concentrations, enzyme molecules are saturated, leading to a plateau in reaction velocity.
Double-Reciprocal Plot (Lineweaver-Burk): A linear plot of 1/v vs. 1/[S] for easier determination of kinetic parameters like Vmax and Km.

DNA Recombinant Technology

Restriction nucleases (enzymes) cleave DNA molecules at specific sequences, allowing for manipulation and analysis of DNA.
This leads to the generation of restriction fragments, DNA pieces with specific lengths.

DNA Electrophoresis: Separating DNA Fragments

DNA electrophoresis separates DNA fragments based on size using a gel matrix and an electric field.
The smaller the fragment, the faster it migrates through the gel.

Southern Blotting: Identifying Specific DNA Sequences

Southern blotting combines the processes of DNA digestion, electrophoresis, and hybridization to identify a specific DNA sequence within a complex mixture.
- DNA is digested with restriction enzymes to create fragments.
- Fragments are separated by size using electrophoresis.
- DNA transferred from the gel to a membrane.
- A labeled probe (single-stranded DNA) complementary to the target sequence hybridizes to the membrane.
- Hybridization can be detected by autoradiography or chemiluminescence.

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Week 7-8