MCB 2050 Final Exam |174 Questions with Answers
What is traditional cell biology? - -the multidisciplinary study of the composition, function,
and structure of the various subcellular organelles and other cellular components in
evolutionarily diverse organisms
-What are some model organisms for cell biologists? - --S. pombe (yeast)
-C. elegans (worm)
-D melanogaster (fruit fly) (easy to manipulate genetically and breeds quickly)
-A. thaliana
-M. musculus (mouse) (genome similarity with humans)
-H. sapiens (humans) (learn the 'normal' role of genes by the study of disease)
-1) Who is responsible for the discovery and development for green fluorescent protein?
2) What can agar plates with bacteria colonies be transformed with? - -1) Tsien,
Shimomura, and Chalfie
2) GFP and/or various other coloured fluorescent protein (eg BFP, YFP, tangerine, Cherry,
etc)
-Transplantation of cells harvested from a GFP-expressing organism can be followed in
what? Example? - --non-GFP expressing illegitimate; in the case of the nervous system,
transplantation of neurons can be monitored for circuit integration
-1) What are the components of bright-field microscopy?
2) What is light diffracted by?
3) What is the image captured by? Elaborate.
4) Can easily manipulate digital images using what? Give an example. - -1) light source,
condenser lens, stage, objective, and ocular lens
2) specimen and undifferentiated light (eg field of view) focused by objective lens
3) digital camera
-more sensitive to low light intensities allowing for living cells to be viewed without photo
(light) damage
-record images as a digital file-different light intensities converted into 2D array of
numbers
4) various computer programs
-eg deconvolution of microscopic (digital) images: computer software designed to remove
background and out-of-focus ('blurry') light (yields increase in contrast and clarity)
-1) What is the primary purpose of microscopy?
2) Does continuing to enlarge the image continue to provide more details?
3) What is the most important aspect of today's microscope?
4) What is resolution? - -1) to generate a magnified, high-quality view of the specimen
2) No- this is 'empty magnification'
3) resolution
,4) the minimum distance that can separate two points that still remain identifiable as
separate points (ie ability to see objects as separate entities)
-1) What are the two factors a resolving microscope depends on?
2) How is the resolution of a microscope maximized?
3) For the resolving limit for most standard brightfield and CLSM, what we will observe?* -
-1) -wavelength (lambda) of illumination light
-numerical aperture (light-gathering qualities of the objective lens and the mounting
medium)
2) -use a shorter wavelength of illuminating light
-increase the numerical aperture
-alter the mounting medium (eg air-->oil)
3) larger organelles (eg nuclei, mitochondria, chloroplasts)
-1) List the following, in order, from greatest limit of resolution to least: electron
microscope, human eye, standard brightfield and CLSM, super resolution CLSM
2) What does Electron micrograph use rather than photons? - -1) human eye, standard
brightfield and CLSM, super resolution CLSM, electron microscope
2) electrons (lower wavelength yields higher resolution)
-Give the principles of fluorescence - --certain atoms can absorb a photon of a certain
wavelength (eg blue light)
-atom's electron becomes 'excited' and moves up to higher energy state
-'excited' electron is highly unstable (loses energy and returns to a 'ground state' by
emitting a photon with a lower energy (ie longer wavelength) (eg red light))
-'emitting' electron has lower energy because some of its energy was initially lost as heat
-1) What are fluorophores?
2) What is an example of a fluorescent protein and what are they used for?
3) What is an example of a small chemical or organic compound and what do they do? - -1)
molecules that can re-emit light following excitation
2) -green fluorescent protein and its derivatives
-used for subcellular localization of proteins
3) floroescein
-assist in staining subcellular structures or macromolecules
-direct and indirect immunofluorescence
-Describe confocal laser scanning microscopy (CLSM) - --similar set up to a standard
brightfield light microscope, but with a few additional features
-one or more lasers allow only certain wavelengths of light to strike and 'excite' the LIVING
specimen (specimen does not need to be 'fixed'-allows for dynamic biological and cellular
processes to be viewed live)
-lasers can penetrate into thicker living specimens
-1) In CLSM, what can laser light be focused on and what does it yield?
,2) What happens to all of the out-of-focus fluorescence from the specimen? What is this
out-of-focus fluorescence?
3) How can the z-sections be viewed? - -1) a single layer (focal plane) within the specimen;
yields a 'z-section' or (optical slice) of the specimen
2) it is excluded- results in image that is less 'blurry'; emitted light from above and below
the focal plane
3) individually, serially, or stacked together (ie a z-stack) as a 3D image
-1) What is Transmission Electron Microscopy used to generate?
2) What is an image formed from?* - -1) highly magnified views of internal (cellular)
structures
2) electrons that are transmitted through a specimen
-What are the structural features of an electron microscope? - --hollow cylindrical
chamber (under vacuum)
-electron gun (applied voltage generates a fine electron beam from the top to the bottom of
the chamber; increased voltage=increased electron speed and increased specimen
penetration, but decreased wavelength and increased resolution)
-electromagnetic lenses ('magnets') (condenser, objective, and projector lenses (magnets);
alter beam of electrons (by adjusting voltage) to allow for control of focus and
magnification)
-viewing screen- image captured by a digital camera
-1) How is an image formed from a beam of electrons?
2) Why does 'scattering' happen? Elaborate.
3) Is specimen preparation for TEM very important?* - -1) when electrons strike the
specimen some are 'scattered' (diffracted) and others are not
2) due to the selectively dense properties of the specimen generated during sample
preparation
-electrons that pass easily through the specimen (non-scattered) or pass outside of the cell
are detected by the camera- appear as white or gray areas
-electron dense areas in the specimen (eg membranes) prevent electrons from being
transmitted to the camera-seen as black areas)
3) Yes
-What are the differences between prokaryotes and eukaryotes?* - --prokaryotes have a
nucleoid, eukaryotes have an enclosed nucleus
-prokaryotes have free ribosomes, eukaryotes have free ribosomes and rough ER
-prokaryotes have no endomembrane system, eukaryotes have a vast, interconnected
endomembrane system
-prokaryotes have no mitochondria, eukaryotes have mitochondria/chloroplasts
-prokaryotes are typically small, eukaryotes are typically larger
-1) In regards to the nucleus, what is the primary difference between prokaryotes and
eukaryotes?
, 2) Briefly describe the main components of the eukaryotic nucleus. - -1) eukaryotes
possess a membrane-bound nucleus, whereas prokaryotes possess a 'region' (nucleoid)
where the chromosome is located
2) nuclear envelope: boundary between cytosol and nucleus
nuclear pores: 'doorways' in nuclear envelope
organized internal nuclear structure
-1) What are the notable characteristics of the nucleus?
2) What are the two main functions of the nucleus? - -1) -irregular shape; typically one/cell
-largest organelle
2) -compartmentalization of the cellular genome and its activities (eg site of DNA
replication, transcription, and RNA processing; site where translation components
(ribosomes, mRNA, tRNA) are synthesized)
-coordination of cellular activities (eg control of metabolism, protein synthesis,
reproduction (cell division, etc)
-1) What makes up the nuclear envelope?
2) What makes up the nuclear content?* - -1) -nuclear membrane, nuclear lamina, and
nuclear pores
2) chromatin, nucleoplasm, nuclear matrix (although this is heavily debated), and nucleolus
-Describe the structure of the nuclear envelope - --has 2 parallel phospholipid bilayers
(separated by intermembrane space)
-outer membrane binds ribosomes and is continuous with RER
-inner membrane: contains unique protein composition distinct from outer membrane, and
has integral membrane proteins that connect to nuclear lamina
-intermembrane space (nuclear envelope lumen) continuous with ER lumen
-inner and outer membranes join at nuclear pores
-What are the functions of the nuclear envelope? Elaborate on each one. - -1) separates
nuclear content from cytoplasm
-genome from cytosol
-transcription from translation
2) acts as a selective barrier
-allows regulated passage of molecules (eg RNA and proteins) between the nucleus and
cytosol
-establishes the composition of the nucleus and regulates gene expression
3) binds nuclear lamina
-provides structural framework for nucleus
-1) Describe the structure of the nuclear lamina
2) Describe the functions of the nuclear lamina - -1) thin meshwork of long filament-like
proteins
-ABC nuclear lamins (related to cytosolic and intermediate filament)
-located on inner surface of nuclear envelope
-bound to inner surface of nuclear envelope
What is traditional cell biology? - -the multidisciplinary study of the composition, function,
and structure of the various subcellular organelles and other cellular components in
evolutionarily diverse organisms
-What are some model organisms for cell biologists? - --S. pombe (yeast)
-C. elegans (worm)
-D melanogaster (fruit fly) (easy to manipulate genetically and breeds quickly)
-A. thaliana
-M. musculus (mouse) (genome similarity with humans)
-H. sapiens (humans) (learn the 'normal' role of genes by the study of disease)
-1) Who is responsible for the discovery and development for green fluorescent protein?
2) What can agar plates with bacteria colonies be transformed with? - -1) Tsien,
Shimomura, and Chalfie
2) GFP and/or various other coloured fluorescent protein (eg BFP, YFP, tangerine, Cherry,
etc)
-Transplantation of cells harvested from a GFP-expressing organism can be followed in
what? Example? - --non-GFP expressing illegitimate; in the case of the nervous system,
transplantation of neurons can be monitored for circuit integration
-1) What are the components of bright-field microscopy?
2) What is light diffracted by?
3) What is the image captured by? Elaborate.
4) Can easily manipulate digital images using what? Give an example. - -1) light source,
condenser lens, stage, objective, and ocular lens
2) specimen and undifferentiated light (eg field of view) focused by objective lens
3) digital camera
-more sensitive to low light intensities allowing for living cells to be viewed without photo
(light) damage
-record images as a digital file-different light intensities converted into 2D array of
numbers
4) various computer programs
-eg deconvolution of microscopic (digital) images: computer software designed to remove
background and out-of-focus ('blurry') light (yields increase in contrast and clarity)
-1) What is the primary purpose of microscopy?
2) Does continuing to enlarge the image continue to provide more details?
3) What is the most important aspect of today's microscope?
4) What is resolution? - -1) to generate a magnified, high-quality view of the specimen
2) No- this is 'empty magnification'
3) resolution
,4) the minimum distance that can separate two points that still remain identifiable as
separate points (ie ability to see objects as separate entities)
-1) What are the two factors a resolving microscope depends on?
2) How is the resolution of a microscope maximized?
3) For the resolving limit for most standard brightfield and CLSM, what we will observe?* -
-1) -wavelength (lambda) of illumination light
-numerical aperture (light-gathering qualities of the objective lens and the mounting
medium)
2) -use a shorter wavelength of illuminating light
-increase the numerical aperture
-alter the mounting medium (eg air-->oil)
3) larger organelles (eg nuclei, mitochondria, chloroplasts)
-1) List the following, in order, from greatest limit of resolution to least: electron
microscope, human eye, standard brightfield and CLSM, super resolution CLSM
2) What does Electron micrograph use rather than photons? - -1) human eye, standard
brightfield and CLSM, super resolution CLSM, electron microscope
2) electrons (lower wavelength yields higher resolution)
-Give the principles of fluorescence - --certain atoms can absorb a photon of a certain
wavelength (eg blue light)
-atom's electron becomes 'excited' and moves up to higher energy state
-'excited' electron is highly unstable (loses energy and returns to a 'ground state' by
emitting a photon with a lower energy (ie longer wavelength) (eg red light))
-'emitting' electron has lower energy because some of its energy was initially lost as heat
-1) What are fluorophores?
2) What is an example of a fluorescent protein and what are they used for?
3) What is an example of a small chemical or organic compound and what do they do? - -1)
molecules that can re-emit light following excitation
2) -green fluorescent protein and its derivatives
-used for subcellular localization of proteins
3) floroescein
-assist in staining subcellular structures or macromolecules
-direct and indirect immunofluorescence
-Describe confocal laser scanning microscopy (CLSM) - --similar set up to a standard
brightfield light microscope, but with a few additional features
-one or more lasers allow only certain wavelengths of light to strike and 'excite' the LIVING
specimen (specimen does not need to be 'fixed'-allows for dynamic biological and cellular
processes to be viewed live)
-lasers can penetrate into thicker living specimens
-1) In CLSM, what can laser light be focused on and what does it yield?
,2) What happens to all of the out-of-focus fluorescence from the specimen? What is this
out-of-focus fluorescence?
3) How can the z-sections be viewed? - -1) a single layer (focal plane) within the specimen;
yields a 'z-section' or (optical slice) of the specimen
2) it is excluded- results in image that is less 'blurry'; emitted light from above and below
the focal plane
3) individually, serially, or stacked together (ie a z-stack) as a 3D image
-1) What is Transmission Electron Microscopy used to generate?
2) What is an image formed from?* - -1) highly magnified views of internal (cellular)
structures
2) electrons that are transmitted through a specimen
-What are the structural features of an electron microscope? - --hollow cylindrical
chamber (under vacuum)
-electron gun (applied voltage generates a fine electron beam from the top to the bottom of
the chamber; increased voltage=increased electron speed and increased specimen
penetration, but decreased wavelength and increased resolution)
-electromagnetic lenses ('magnets') (condenser, objective, and projector lenses (magnets);
alter beam of electrons (by adjusting voltage) to allow for control of focus and
magnification)
-viewing screen- image captured by a digital camera
-1) How is an image formed from a beam of electrons?
2) Why does 'scattering' happen? Elaborate.
3) Is specimen preparation for TEM very important?* - -1) when electrons strike the
specimen some are 'scattered' (diffracted) and others are not
2) due to the selectively dense properties of the specimen generated during sample
preparation
-electrons that pass easily through the specimen (non-scattered) or pass outside of the cell
are detected by the camera- appear as white or gray areas
-electron dense areas in the specimen (eg membranes) prevent electrons from being
transmitted to the camera-seen as black areas)
3) Yes
-What are the differences between prokaryotes and eukaryotes?* - --prokaryotes have a
nucleoid, eukaryotes have an enclosed nucleus
-prokaryotes have free ribosomes, eukaryotes have free ribosomes and rough ER
-prokaryotes have no endomembrane system, eukaryotes have a vast, interconnected
endomembrane system
-prokaryotes have no mitochondria, eukaryotes have mitochondria/chloroplasts
-prokaryotes are typically small, eukaryotes are typically larger
-1) In regards to the nucleus, what is the primary difference between prokaryotes and
eukaryotes?
, 2) Briefly describe the main components of the eukaryotic nucleus. - -1) eukaryotes
possess a membrane-bound nucleus, whereas prokaryotes possess a 'region' (nucleoid)
where the chromosome is located
2) nuclear envelope: boundary between cytosol and nucleus
nuclear pores: 'doorways' in nuclear envelope
organized internal nuclear structure
-1) What are the notable characteristics of the nucleus?
2) What are the two main functions of the nucleus? - -1) -irregular shape; typically one/cell
-largest organelle
2) -compartmentalization of the cellular genome and its activities (eg site of DNA
replication, transcription, and RNA processing; site where translation components
(ribosomes, mRNA, tRNA) are synthesized)
-coordination of cellular activities (eg control of metabolism, protein synthesis,
reproduction (cell division, etc)
-1) What makes up the nuclear envelope?
2) What makes up the nuclear content?* - -1) -nuclear membrane, nuclear lamina, and
nuclear pores
2) chromatin, nucleoplasm, nuclear matrix (although this is heavily debated), and nucleolus
-Describe the structure of the nuclear envelope - --has 2 parallel phospholipid bilayers
(separated by intermembrane space)
-outer membrane binds ribosomes and is continuous with RER
-inner membrane: contains unique protein composition distinct from outer membrane, and
has integral membrane proteins that connect to nuclear lamina
-intermembrane space (nuclear envelope lumen) continuous with ER lumen
-inner and outer membranes join at nuclear pores
-What are the functions of the nuclear envelope? Elaborate on each one. - -1) separates
nuclear content from cytoplasm
-genome from cytosol
-transcription from translation
2) acts as a selective barrier
-allows regulated passage of molecules (eg RNA and proteins) between the nucleus and
cytosol
-establishes the composition of the nucleus and regulates gene expression
3) binds nuclear lamina
-provides structural framework for nucleus
-1) Describe the structure of the nuclear lamina
2) Describe the functions of the nuclear lamina - -1) thin meshwork of long filament-like
proteins
-ABC nuclear lamins (related to cytosolic and intermediate filament)
-located on inner surface of nuclear envelope
-bound to inner surface of nuclear envelope
