Cell biology exam 1

Centrifugation

a technique used to separate molecules or cellular components based on their physical properties, primarily through the use of centrifugal force

Ion exchange chromatography

method used to separate proteins based on their surface charge

Gel-filtration Chromatography

also known as size-exclusion chromatography, is a technique that separates proteins based on their size

Affinity chromatography

technique used to purify specific proteins from a complex mixture based on their unique binding properties.

Native gel electrophoresis

separates proteins based on their size, charge, and shape while maintaining their native structure and interactions

SDS-Page electrophoresis

a technique used to separate proteins based primarily on their molecular weight. It involves the use of the detergent to denature proteins and give them a uniform negative charge

(IEF) Isoelectric focusing

a type of electrophoresis that separates proteins based on their isoelectric point (pI), which is the pH at which the protein has no net electrical charge

Western blotting

is a technique used to detect specific proteins within a sample after they have been separated by gel electrophoresis

Co-immunoprecipitation

a technique used to identify protein-protein interactions by using an antibody to pull a specific protein (and its binding partners) out of a complex mixture

Epitope tagging

adding a short, known peptide sequence (the epitope tag) to a protein of interest

Affinity tagging

adding a specific peptide sequence (the affinity tag) to the protein of interest. This tag is designed to bind to a specific substrate

Forward genetics

begins with a phenotype of interest and works towards identifying the gene

Reverse Genetics

begins with a specific gene and works towards identifying the phenotype

Population genetics

a way of studying genetic variation within and between populations, and can be used to infer how genes are associated with certain traits or diseases

Amphiphilic

a molecule that has both hydrophilic (water-attracting) and lipophilic (or hydrophobic, water-repelling) domains

Phospholipid Bilayer

structure formed by two layers of phospholipid molecules, which is the basic structure of biological membranes

lipid rafts

dynamic, specialized microdomains within the cell membrane that are characterized by a distinct lipid composition and may have specific functions in cell signaling and membrane protein localization

Integral membrane proteins

a type of protein that is permanently attached to the cell membrane

Peripheral membrane proteins

a type of protein that is temporarily associated with the cell membrane or with other membrane proteins, but it is not embedded within the lipid bilayer

(FRAP) Fluorescence recovery after photobleaching

a technique used to study the mobility of molecules, particularly proteins, within a cell membrane It involves using fluorescence microscopy and photobleaching to track the movement of fluorescently labeled molecules

Homeoviscous adaptation

a process by which cells maintain the fluidity of their membranes by altering the composition of their lipids in response to temperature changes

Microfilaments

also known as actin filaments, are a major component of the cytoskeleton

G-Actin

G-actin, or globular actin, is the monomeric form of actin that, when assembled, forms microfilaments also known as F-actin

F-Actin

F-actin, or filamentous actin, refers to the polymeric form of actin that makes up microfilaments, a major component of the cell's cytoskeleton

Nucleation

the initial step in the formation of a new actin or microtubule filament, and is generally considered the rate-limiting step

Polymerization

the process by which monomers are added to a growing filament, and is a key step in the formation of both actin microfilaments and microtubules

Treadmilling

dynamic process observed in actin filaments where G-actin monomers are added to the plus end of the filament while other G-actin monomers are simultaneously removed from the minus end

Profilin

a key regulatory protein that plays a significant role in actin polymerization by promoting the addition of G-actin monomers to the plus end of actin filaments

Thymosin

a regulatory protein that plays a role in actin dynamics by binding to G-actin monomers and preventing them from being added to actin filaments

Formin

a class of proteins that play a crucial role in actin polymerization by working in conjunction with profilin to promote both the nucleation and elongation of actin filaments

CapZ

a regulatory protein that controls actin filament length by preventing the addition or loss of monomers at the plus end of actin filaments

Tropomodulin

a regulatory protein that controls actin filament length by preventing the addition or loss of monomers at the minus end of actin filaments

Cofilin

a regulatory protein that plays a crucial role in actin dynamics by promoting the disassembly of actin filaments

Tropomyosin

regulatory protein that plays a crucial role in stabilizing actin filaments by binding along their length

Arp2/3

a protein complex that plays a crucial role in actin dynamics by initiating actin filament branching and nucleation

Microtubules

a key component of the cytoskeleton, and they are involved in a variety of cellular processes. They are more rigid and less flexible than intermediate filaments, and they are different from actin filaments, which are also part of the cytoskeleton

α-tubulin

a key protein that, along with β-tubulin, forms the basic building block of microtubules

β-tubulin

a key protein that, along with α-tubulin, forms the basic building block of microtubules

γ-Tubulin

a crucial protein involved in the nucleation of microtubules at the Microtubule Organizing Centers (MTOCs), or centrosomes

γ-TuRC (gamma-tubulin ring complex)

a crucial protein complex that plays a key role in the nucleation of microtubules at the Microtubule Organizing Centers (MTOCs) It is essential for the proper organization of the microtubule network within the cell

Catastrophe

a term that describes a key aspect of microtubule dynamics. It refers to the rapid shrinking of a microtubule due to the hydrolysis of GTP on β-tubulin

Rescue

a term that describes a key aspect of microtubule dynamics, referring to the process where a shrinking microtubule switches back to a growth phase. This is crucial for the dynamic instability of microtubules, allowing them to perform their various cellular functions

Microtubule Organizing centers (MTOCs) or centrosomes

also known as the centrosome, is a crucial structure in the cell that serves as the primary site for the nucleation of microtubules

Centrioles

proteinaceous structures that are a key component of the Microtubule Organizing Center (MTOC), also known as the centrosome, and play a crucial role in cell division and the organization of the microtubule network

Intermediate filaments

a major component of the cytoskeleton, distinct from actin filaments and microtubules, and are best thought of as cellular ropes that provide mechanical strength and flexibility to cells and tissue

Molecular motors

proteins that undergo conformational changes to catalyze effects, especially movement, within a cell, Cytoskeletal motors are a specific class that move along actin filaments or microtubules, and include myosins, kinesins, and dyneins

Myosin

a class of actin-binding molecular motors that use the energy of ATP hydrolysis to generate force and movement. They play crucial roles in various cellular processes, including muscle contraction, vesicle transport, and cell motility

Myosin I

primarily involved in vesicle transport. It is characterized as a non-processive, plus-ended motor

Myosin II

primarily known for its role in muscle contraction, but also participates in other cellular processes. It is characterized as a non-processive, plus-ended motor

Myosin V

primarily involved in vesicle transport. It is characterized as a processive, plus-ended motor

Myosin VI

primarily involved in vesicle transport. It is unique among myosins as it is a processive, minus-ended motor

Kinesin

a type of microtubule-binding molecular motor protein that is primarily involved in intracellular transport. Kinesin is a processive, plus-ended motor protein

Dynein

a type of microtubule-binding molecular motor protein that is primarily involved in intracellular transport. It is characterized as a processive, minus-ended motor protein

Processive motor

a molecular motor that remains attached to its cytoskeletal filament as it moves, allowing it to take multiple steps without detaching

Non-processive motor

a molecular motor that detaches from its cytoskeletal filament during its movement, meaning it must repeatedly bind, move, and then release the filament as it transports cargo

Cadherin

a family of cell-cell adhesion proteins that play a crucial role in the organization of tissues and in development

Adherens junctions

a type of cell-cell junction that are primarily responsible for the adhesion of cells to one another through the binding of cadherin proteins

Desmosomes

a type of cell-cell junction that provide strong adhesion between cells through connections with intermediate filaments. They are critical for maintaining the structural integrity of tissues that experience mechanical stress.

Integrins

Focal Adhesions

Hemidesmosomes

Extracellular Matrix (ECM)

Tight junctions

Gap Junctions

Nucleolus

snoRNPs

heterochromatin

Euchromatin

Nuclear Envelope

Nuclear Lamina

LINC Complex (Linker of nucleoskeleton and cytoskeleton)

Dimer

a structure formed by two subunits of a molecule, often a protein, that are bound together

Fusion protein

How to make polyclonal antibodies

How to make monoclonal antibodies

Antigen

Antibody

Widefield Microscopy

Confocal Microscopy

Distance is equal to?

λ/2

2 limitations of light microscopy

Resolution, lack of detail

3 ways to label proteins

Antibodies, Fusion proteins, Epitope tagging

Constant region (antibody)

Variable region (antibody)

Antibody structure

Secondary antibody

GFP

Cell Fractionation

Velocity Sedimentation

Beta-mercaptoethanol and DTT

GST binds with

Glutathione

His binds with

Cations (Nickel)

Biotin binds with

Streptavidin

3 ways phospholipids differ

Tail length, Saturation, head groups

Why does a phospholipid bilayer membrane require no energy to form?

Energetically favorable, Steric hindrance

3 things that affect membrane fluidity

Temperature, Cholesterol, and fatty acid saturation (unsaturation increases fluidity)

How many amino acids does it take to traverse the membrane

~20

hydrophathy plot

4 ways to limit protein mobility

Bind “scaffolding” proteins, fences, binding to other cells, and lipid rafts.