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A cell

Structural and functional fundamental unit of life characterized by self-regulation

Types of cells

Eukaryotic cells (plants

Organelle

Intracellular complex with specialized morphology and function

Membrane-bound organelles

Peroxisomes

Peroxisome

Performs oxidative reactions

Lysosome

Contains digestive enzymes and degrades macromolecules

Endoplasmic reticulum

Responsible for calcium storage and lipid and protein biosynthesis

Golgi apparatus

Modifies

Nucleus

Largest membrane-bound organelle in mammals that stores genetic material and performs transcription

Non-membrane-bound organelles

Cytoskeleton

Cytoskeleton

Network of fibrillary proteins that maintains cell shape

Ribosome

Site of protein synthesis where mRNA is translated

Proteasome

Digests cytosolic proteins

Centrioles

Organize the microtubule network and mitotic spindle

Main components of a eukaryotic cell

Cell membrane

Stem cell

Immature

Cytoplasmic inclusions

Lipid droplets and glycogen inclusions that do not perform metabolic activities

In vivo study

Study of cells or tissues within an intact living organism

Advantage of in vivo studies

Results closely reflect biological processes in the whole organism

Limitation of in vivo studies

Experimental results are influenced by multiple components of the organism

In vitro study

Study of cells or biological processes outside the organism in a controlled environment

Advantages of in vitro studies

Rigorous control of experimental conditions

Limitation of in vitro studies

Results may not fully reflect what occurs in a living organism

Preclinical studies

Studies that investigate disease mechanisms and test efficacy and toxicity of drugs before clinical use

Components of preclinical studies

Genetic testing

Permanent microscopy specimen preparation

Harvesting

Fixation

Preservation of tissues and cells to prevent autolysis and maintain architecture

Chemical fixation

Preservation using fixatives such as formaldehyde

Physical fixation

Preservation by freezing

Hematoxylin

Basic dye that stains acidic structures such as nuclei purple-blue

Eosin

Acidic dye that stains basic structures such as cytoplasm pink

Bright-field microscopy

Light microscopy in which contrast is enhanced using conventional dyes

Phase-contrast microscopy

Light microscopy in which contrast is enhanced by differences in light refraction

Fluorescence microscopy

Light microscopy using fluorescent labels to generate contrast

Magnification of a light microscope

Magnification of objective lens multiplied by magnification of eyepiece

4× objective

Used to locate the specimen

10× objective

Used to identify the area of interest

20×/40× objective

Used to identify tissue type

60×/100× objective

Used to identify cell type

Resolution

Minimum distance at which two points can be distinguished as separate entities

Factors affecting LM resolution

Refractive index

Physical limit of LM resolution

Approximately 0.2 μm

Electron microscope capabilities

Measured by magnification and resolution

Ultrastructure

Fine structural details visible only by electron microscopy

TEM principle

Electrons pass through a thin specimen and are detected to produce a high-resolution image of internal structures

Electron-dense area

Dark region where few electrons pass through

Electron-lucent area

Light region where many electrons pass through

Antibody

Y-shaped protein produced by B lymphocytes that specifically binds an antigen

Antigen

Molecule capable of stimulating antibody production

Methods using antibodies

Immunolabeling and ELISA

Immunolabeling

Detection technique based on specific antigen-antibody interactions using labeled antibodies

Detection labels in immunolabeling

Enzymes and fluorescent molecules

ELISA

Technique using enzyme-linked antibodies to quantify antigens by color intensity

Central dogma

Flow of genetic information from DNA to RNA to protein

Methods for studying nucleic acids

PCR and gene sequencing

PCR

Technique used to amplify a specific DNA sequence

RT-PCR

Technique in which RNA is converted to cDNA and then amplified by PCR

Gene sequencing

Determination of the exact order of nucleotides in DNA

Primary protein structure

Linear sequence of amino acids

Secondary protein structure

Local folding patterns such as alpha helices and beta sheets

Tertiary protein structure

Three-dimensional folding of an entire protein

Main classes of proteins

Enzymes

Cell culture

Maintenance of viable cells in controlled laboratory conditions

Importance of cell culture

Useful for studying cell function

Advantage of animal models

More closely resemble human disease and physiology than cell cultures

TEM fixation methods

Chemical fixation and cryofixation

Negative staining

TEM preparation method for viruses and proteins

Cryo-EM

Electron microscopy of rapidly frozen specimens in vitreous ice

SEM

Electron microscopy used to visualize surface morphology and three-dimensional structures

Specialized cell

Cell with structural adaptations and organelle development optimized for a specific function

Immunohistochemistry

Immunolabeling technique using antibodies linked to visible markers to detect proteins in tissues

Mobile cilium ultrastructure

Axoneme composed of 9 peripheral microtubule doublets and 2 central microtubules anchored to a basal body

Rough endoplasmic reticulum

Ribosome-studded membrane network involved in synthesis and processing of proteins

Nuclear envelope

Double membrane surrounding the nucleus that maintains nuclear integrity

Euchromatin

Pale-staining chromatin that is transcriptionally active

Structure in microscopy

Morphological organization of cells or tissues visible under a microscope

X-ray crystallography

Technique that determines the three-dimensional arrangement of atoms within a crystal

Ribosome structure

Ribonucleoprotein organelle composed of large and small subunits assembled on mRNA

Mitochondrial function

Production of ATP through cellular respiration

Functions of the cytoskeleton

Maintenance of cell shape

Passive transport

Movement of molecules down a concentration gradient without energy expenditure

Active transport

Movement of molecules against a concentration gradient using energy

Selective barrier function of plasma membrane

Hydrophobic phospholipid bilayer restricts passage of polar and charged molecules while allowing selective transport

Cell communication

Signaling through chemical molecules or conversion of physical stimuli into intracellular signals

Endocytic pathway

Internalization of extracellular material into vesicles that fuse with lysosomes for digestion

Lysosomal digestion

Breakdown of internalized material by acid hydrolases within lysosomes

Cell-cycle checkpoint

Regulatory threshold determining whether a cell proceeds through the cell cycle or pauses

Gap junction

Communication junction formed by connexons allowing passage of ions and small molecules between adjacent cells

Promoter methylation

Epigenetic modification that generally suppresses gene transcription

Exocytosis

Final step of the secretory pathway involving release of vesicle contents outside the cell

Facilitated diffusion

Passive transport mediated by carrier proteins or channels

Signal recognition particle (SRP)

Complex that directs proteins containing an ER signal sequence to the rough ER

Smooth endoplasmic reticulum detoxification

Conversion of lipid-soluble drugs and metabolites into water-soluble forms for excretion

Mitochondrial genome significance

Maternal inheritance of mitochondrial DNA mutations that can cause severe diseases

Primary cilium

Non-motile cilium involved in sensing and responding to extracellular signals

Two-dimensional membrane fluidity

Produced by lateral and rotational movement of membrane lipids

Nucleolus

Site of ribosomal subunit biogenesis and assembly of signal recognition particles

Lysosomal storage disease

Genetic disorder caused by deficiency of lysosomal hydrolases leading to substrate accumulation

Genome vs proteome

Proteome is more complex than the genome due to transcriptional and post-translational modifications. Here are the additional cards that were missing from the previous version based on your notes. Add these to the end of the deck.

Specialized cell

Intestinal absorptive cell

Specialized cell with numerous microvilli that increase surface area for nutrient absorption