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Cellular Organelles and Microscopy Techniques Study Guide

This guide delves into the intricate structure of chromatin, the complex of DNA and proteins that forms chromosomes within eukaryotic cells. It covers the basic units of chromatin, such as nucleosomes and histones, and progresses to higher-order structures like 30 nm fibers and mitotic chromosomes. The guide also differentiates between euchromatin and heterochromatin, explaining their distinct roles in regulating gene accessibility and expression. Key concepts include the function of histone pro

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Energy Production and Metabolic Processes

Mitochondrial Energy Production and Photosynthesis

Mitochondria and chloroplasts utilize proton gradients, electron transport chains, and membrane systems to drive ATP production through oxidative phosphorylation and photosynthesis.

Mitochondrial structure
Oxidative phosphorylation
Electron transport chain
ATP synthase
Glycolysis
Citric acid cycle
Proton gradient
Inhibitors and uncouplers
Mitochondrial disorders
Endosymbiont theory
Photosynthesis
Light reactions

Mitochondrial Structure and Cellular Respiration

Mitochondrial morphology
Fusion and fission
Double-membrane system
Mitochondrial matrix
Oxidative phosphorylation
Electron transport chain
ATP synthase
Citric acid cycle
Glycolysis
Fermentation
NADH and FADH2
Proton gradient

Lipid Metabolism and Beta Oxidation

Lipids as an energy source
Triglycerides
Free fatty acids
Carnitine shuttle
CPT I
Lipase
Beta-oxidation
ATP yield
Lipolysis
Carnitine deficiency
MCAD deficiency
Diabetic ketoacidosis
Ketone body production

Electron Transport Chain and ATP Synthesis

Electron transport chain complexes
NADH dehydrogenase
Succinate dehydrogenase
Ubiquinone
Cytochrome b-c1 complex
Cytochrome c
Cytochrome oxidase
Proton gradient
ATP synthase
Metabolic poisons
Uncoupling proteins
Mitochondrial disorders
MERRF disorder

Mitochondria, Chloroplasts, and Photosynthetic Processes

This content explores the endosymbiont theory, mitochondrial function, and the mechanisms of photosynthesis including light reactions and the Calvin cycle.

Endosymbiont theory
Mitochondrial DNA mutations
Photosynthesis light reactions
Photosynthetic carbon-fixation reactions
Photosystems I and II
Electron transport chain
ATP synthesis
Chloroplast structure
Mitochondrial oxidative phosphorylation

Microscopy Techniques and Cellular Analysis Methods

Cellular Organelles and Microscopy Techniques

An overview of the endomembrane system, organelle functions, microscopy optical pathways, and subcellular fractionation methods.

Endomembrane System
Endoplasmic Reticulum
Rough ER
Smooth ER
Golgi Apparatus
Lysosomes
Peroxisomes
Compound Microscope
Resolution
Numerical Aperture
Brightfield Microscopy
Phase-Contrast Microscopy
Transmission Electron Microscopy
Fluorescence Microscopy
Subcellular Fractionation
Differential Centrifugation
Equilibrium Density-Gradient Centrifugation
Western blot analysis

Protein Analysis and Separation Techniques

Methods for examining proteins in cell extracts include enzymatic assays, western blot analysis, polyacrylamide gel electrophoresis, and various chromatography procedures.

Enzymatic assays
Western blot analysis
Polyacrylamide gel electrophoresis
Native gel electrophoresis
SDS-polyacrylamide gel electrophoresis
Ion-exchange chromatography
Size exclusion chromatography
Affinity chromatography
Immunoprecipitation
Protein interactions

Molecular Biology Techniques and Gene Silencing

Methods including yeast two-hybrid, FRET, and RNA interference are used to examine protein-protein interactions and assess protein function.

Yeast two-hybrid
Transcription factor reconstitution
Reporter gene expression
FRET (fluorescence resonance energy transfer)
Protein-protein interactions
Central dogma of molecular biology
RNA interference (RNAi)
Dicer
RISC (RNA-induced silencing complex)
Argonaute
Protein knockdown

Studying Cells with Compound Microscopes

The compound microscope contains several lenses that magnify the image of a specimen through an optical pathway.

compound microscope
optical pathway
light source
objective lens
ocular lens
eyepiece
specimen magnification

Microscopy Magnification and Resolution Principles

The relationship between total magnification, resolving power, wavelength, refractive index, and different types of light microscopy.

total magnification
resolving power
resolution (D)
objective lens
ocular lens
wavelength
refractive index
diffraction
brightfield microscopy
phase-contrast microscopy
interference contrast (DIC)
immersion oil

Transmission Electron Microscope Principles and Components

Transmission electron microscopes use electrons instead of light to form images and provide higher resolution compared to light microscopes.

Transmission electron microscope (TEM)
Light microscope
Electromagnetic coils
Vacuum
Cathode
Electromagnetic condenser lens
Ultramicrotome
Electromagnetic objective lens
Electromagnetic projector lens
Specimen detector
Resolution

Microscopy Resolution and Fluorescence Principles

The limits of resolution, the sizes of cells and of their component parts, and the three-stage process of fluorescence microscopy.

Limits of resolution
Cell and organelle sizes
Fluorescence microscopy
Excitation wavelength
Emission wavelength
Fluorescence three-stage process
Energy dissipation
Optical path in fluorescence microscopy
Barrier filters
Fluorescein
Tetramethylrhodamine

Fluorescence Microscopy and Cell Culture Techniques

This content covers confocal microscopy, immunofluorescence, immunogold electron microscopy, and methods for cell culture and sorting.

Confocal microscopy
Conventional fluorescence microscopy
Immunofluorescence microscopy
Primary antibody
Secondary antibody
Fixation
Permeabilization
Immunogold electron microscopy
Green fluorescent protein (GFP)
Tissue culture
Fluorescence-activated cell sorting (FACS)
Confluency
Primary cells
Cell line
Transformed cell line

Cellular Structure, Organization, and Fractionation

Basic Properties and Organization of Cells

Cells are autonomous units of life characterized by complexity, regulation, genetic programs, and the ability to acquire energy and carry out metabolism.

Basic properties of cells
Cellular organization levels
Genetic information and DNA
Cellular reproduction
Energy acquisition and ATP production
Metabolism including catabolism and anabolism
Prokaryotic vs eukaryotic cells
Nucleus structure and function
Mitochondrial morphology and dynamics

Subcellular Fractionation and Cell Disruption

Subcellular fractionation involves the separation of the cell into functioning organelles or isolation of individual organelles through cell disruption in an isotonic solution.

Subcellular fractionation
Isotonic solution
Hypotonic solution
Hypertonic solution
Cell disruption
Homogenate
Microsomes
Sonication
Mechanical homogenizer
Organelle isolation

Subcellular Fractionation and Organelle Centrifugation

Subcellular fractionation procedures use differential centrifugation and equilibrium density-gradient centrifugation to separate organelles based on size and density.

differential centrifugation
equilibrium density-gradient centrifugation
sedimentation
pellet
supernatant
ultracentrifuge
centrifugal force
organelle density
sucrose gradient
microsomes
plasma membrane vesicles
post-nuclear supernatant

Introduction to Cells and Organelles

The study of cells and their structure, function and behaviour, including the distinction between prokaryotic and eukaryotic cells.

Cell biology
Fundamental unit of life
Organelles
Cellular organization
Prokaryotic cells
Eukaryotic cells
DNA
Nucleoid
Nucleus
Cytoplasm
Ribosomes
Plasma membrane
ATP
Metabolism
Mitosis
Simple fission

Structure and Function of the Nucleus

The nucleus contains DNA and is surrounded by a nuclear envelope consisting of the nuclear lamina and nuclear pore complexes that regulate nucleocytoplasmic trafficking.

Nucleus
DNA
Nuclear envelope
Nuclear lamina
Nuclear pore complexes
Nucleocytoplasmic trafficking
Importins
Ran-GTP
Nuclear localization signal
Nucleolus
Ribosome assembly
Ribosomal subunits

Chromatin Structure and Organization

Chromatin consists of eukaryotic DNA and proteins, including histones and nonhistone chromosomal proteins, organized into nucleosomes and higher-ordered structures.

Chromatin
Histones
Nucleosome
Nucleosome core particle
Linker DNA
30 nm fibers
Supercoiled loops
Mitotic chromosomes
Karyotype
Euchromatin
Heterochromatin
Constitutive heterochromatin
Facultative heterochromatin

Cells, Organelles, and the Endomembrane System

The endomembrane system includes organelles such as the endoplasmic reticulum, Golgi complex, endosomes, lysosomes, and vacuoles functioning as a coordinated unit.

endoplasmic reticulum
rough ER
smooth ER
transitional ER
Golgi apparatus
cis Golgi network
trans Golgi network
cisternae
transport vesicles
protein glycosylation
lipid synthesis
quality control
unfolded protein response
ER-associated degradation
cisternal maturation
vesicular transport

Lysosomes, Peroxisomes, and the Cytoskeleton

This content explores the structure and function of lysosomes, peroxisomes, and the cytoskeleton, including their roles in degradation, oxidation, and cellular movement.

Lysosomes
Acid hydrolases
Autophagy
Endocytosis
Phagocytosis
Lysosomal storage diseases
Peroxisomes
Hydrogen peroxide oxidation
Plasmalogen biosynthesis
Cytoskeleton
Microtubules
Actin filaments
Intermediate filaments

Cell Biology Midterm Examination Practice

Examination questions covering cell biology topics including microscopy, organelles, and the endomembrane system.

light microscopy resolution
immunogold electron microscopy
nuclear pore complexes
nucleolus
ribosome protein synthesis
mitochondrial electron transfer chain
ATP synthase
thylakoid membrane electron transfer
rough endoplasmic reticulum
smooth endoplasmic reticulum
Golgi apparatus
cytoskeleton
electron microscope electromagnetic lenses
endomembrane system
lysosome delivery pathways
subcellular fractionation
ultracentrifuge vacuum system

Biological Membrane Structure, Composition, and Function

Biological Membrane Structure and Function

Biological membranes consist of a lipid bilayer and proteins that perform functions including compartmentalization, selective permeability, and signal transduction.

Fluid-mosaic model
Selective permeability
Compartmentalization
Signal transduction
Intercellular interaction
Amphipathic nature of lipids
Phosphoglycerides
Sphingolipids
Cholesterol
Membrane fluidity
Lateral diffusion
Fluorescence Recovery After Photobleaching (FRAP)
Flippases and scramblases
Phospholipase activity

Cell Biology Membrane Structure and Functions

Biological membranes are composed of lipids and proteins that form a lipid bilayer to provide compartmentalization, selective permeability, and energy transduction.

fluid-mosaic model
selective permeability
compartmentalization
membrane proteins
energy transduction
plasma membrane
organelle membranes
sandwich model

Chemical Composition of Membrane Lipids

Molecules with both hydrophilic and hydrophobic properties are termed amphipathic, including phosphoglycerides, sphingolipids, and cholesterol.

hydrophilic head
hydrophobic tail
fatty acids
saturated fatty acids
unsaturated fatty acids
phosphoglycerides
sphingolipids
cholesterol
phospholipids
glycerol
ester linkages
phosphatidylcholine
phosphatidylethanolamine
phosphatidylserine
phosphatidylinositol
sphingomyelin

Lipid Bilayer Structure and Membrane Fluidity

The lipid bilayer behaves as a two-dimensional fluid where membrane fluidity is determined by lipid mobility, hydrocarbon tail length, saturation, and cholesterol.

hydrophobic molecules
micelles
bilayers
liposomes
lateral diffusion
rotation
flip-flop
flippases
cholesterol
fluorescence recovery after photobleaching
hydration shell
hydrocarbon tails
saturation
unsaturated hydrocarbon tails
phosphatidylethanolamine
phosphatidylcholine
phosphatidylinositol

Asymmetric Distribution of Plasma Membrane Lipids

Asymmetric distribution of lipids in the plasma membrane is maintained by flippases and scramblase during lipid synthesis and transfer between compartments.

Asymmetric distribution of lipids
Plasma membrane leaflets
Flippases
Scramblase
Phosphoglycerides
Phosphatidylcholine
Phosphatidylserine
Phosphatidylethanolamine
Phosphatidylinositols
Sphingomyelin
Glycolipids
Cholesterol
Phospholipases
Phospholipase D
Phospholipase A1
Phospholipase A2

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