Lecture 2 - Exam 1 Flashcards

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1
Q

Describe what happens in endosymbiosis.

A

Archaea engulfed a bacteria cell. Endosymbiosis occurred and most genes of endocytosed bacterium are transferred to host genome. Form new eukaryotic cell with a nucleus and mitochondria.

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2
Q

An RNA molecule can catalyze what?

A

Its own synthesis.

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3
Q

What does model systems refer to?

A

A non-human species that is extensively studied to understand particular biological phenomena present in many related organisms.

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4
Q

While studies of model systems are important to science, only human studies are beneficial to medical research. T or F.

A

False. Many metabolic pathways, developmental patterns, and even genes are shared across microbe, plant, and animal groups.

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5
Q

T or F. Stuff learned from experiments performed by one cell type are generally applicable to other cells (some animals may be better for certain questions you’re asking in research, though b/c of the great diversity in the types of cells any organism contains).

A

True.

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6
Q

Describe E. Coli as a model organism.

A

Excellent models for fundamental aspects of biochemistry and molecular biology because of their comparative simplicity.
They are easy to grow in the lab.
Small genome.
Can make 108 cells from one single cell overnight.

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7
Q

What are the concepts of molecular biology that come from E. coli?

A

DNA replication, the genetic code, gene expression, and protein synthesis.

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8
Q

Describe Yeast as a model organism.

A

Have many of the experimental advantages of E. coli and have provided many insights into eukaryotic cell biology.
Easy to grow and study in the lab.
Small genome.
Can easily grow lots of cells from one single cell over night.

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9
Q

What are the fundamental concepts of eukaryotic cells that have been discovered in yeast?

A

DNA replication, transcription, RNA processing protein sorting, and cell division.

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10
Q

Describe plant models.

A

Allow us to understand plant development and physiological mechanisms that are of considerable economic importance and intellectual interest.
Most common: Arabodopsis thalania b/c it has the same qualities as Drosophila and C. elegans.
Smallish genome, easy to grow.

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11
Q

What are metazoans?

A

Multicellular animals that pass through embryonic stages of development.

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12
Q

The classification of multicellular organisms depends on?

A

The patterns of their development.
There are 35 metazoan phyla, meaning there are 35 patterns of development that still exist

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13
Q

Describe Vertebrate models.

A

The most complex animals are vertebrates, including humans and other mammals.
Human genome is large.
Complexity makes it hard to study vertebrates.

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14
Q

Describe Protostome model organisms.

A

These are insects, snails, flatworms, etc.
Started when vast numbers of genes for the Drosophila body plan formation were characterized. Remarkably, most of these genes are the same ones used in similar processes in most animals, including us.

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15
Q

Why is so important to use the fruit fly as a model organism for a lot of experiments?

A

They are easy to breed, hardy, and we can use forward genetics.

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16
Q

What are forward genetics?

A

This means generating a random mutation, often with radiation, and after subsequent breeding, isolating individuals with a weird phenotype.

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17
Q

What are some of the powerful things that have come from forward genetics in fruit flies?

A

Sonic Hedgehog signaling pathway & learning about fetal alcohol syndrome.

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18
Q

Describe invertebrate models.

A

Allow us to understand the development of multicellular organisms as well as disease. For example: Sea Urchin. Vertebrates are too complex to study, so these organisms are another good way to study similar genes.

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19
Q

What is a deuterostome? What organisms are classified as such?

A

A deuterostome is characterized by its anus forming before the mouth during embryonic development.
EX: Sea Urchins, humans, and frogs!!

20
Q

An example of similar embryonic development steps are seen in what organisms?

A

Sea Urchins and Frogs. Their life cycles share the basic steps.
First stages are conserved among many organisms, so we can use these models to study the early stages of life!

21
Q

The different embryos of organisms photo in the powerpoint represents what? Out of the organisms in that photo, what two organisms are strikingly similar throughout the entire development process?

A

Epigenesis, meaning the first stage of embryonic development is similar, and then the organisms will diverge and differentiate.
The fish and salamander look very similar throughout the whole development.

22
Q

Are zebrafish a good vertebrate model?

A

Yes! Their development in 24 hours is very helpful in research.

23
Q

What are some examples of amniote vertebrates? What are they used for?

A

Chickens and mice are used to study later stages of human life.

24
Q

What are some of the fundamental concepts of mammalian cell biology discovered in cell culture?

A

DNA replication, gene expression, protein synthesis & processing, protein sorting, cell division, cell-to-cell signaling.

25
Q

What is the process for culturing animal cells?

A

Piece of tissue is dispersed in a suspension of individual cells. Cell suspension will occur.
The cells are plated in a culture dish in nutrient liquid medium.
The cells in the primary culture attach to the dish and grow until they cover the culture dish surface.
The cells can then be removed from the culture dish and replated at a lower density to form a secondary culture.

26
Q

What are the tools of cell biology?

A

Schematic representation: often presented in books and useful for pedagogic purposes. Not accurate, over-simplified.
Modern light microscopes: can magnify objects up to about 1000X. Can see cells between 1-100um & can see some organelles (nucleus, mitochondria), & is an affordable microscope!

27
Q

When we look through a light microscope, what is happening?

A

Light from a mirror is reflected up through the specimen, into objective lens to produce first magnification. The image produced by the objective lens is then magnified again by the eye piece lens (simple magnification set at 10x).

28
Q

In a light microscope, what is the resolution equation?

A

Resolution = (0.61) (wavelength of visible light) / numerical aperture
Numerical aperture in air = 1
Add oil and it increases to 1.4
On slides:
Resolution = (0.61 x 0.5) / 1.4 = 0.22uM

29
Q

If the resolution of a light microscope is 0.22 uM, what does that mean for the quality of the image?

A

Can only get down to about 0.22 uM before things start blurring together.

30
Q

What is the light microscopes limitation?

A

Resolution, due to wavelength of visible light.

31
Q

What is brightfield microscopy?

A

One of the most basic light microscopy techniques whereby the sample is illuminated by white light that is transmitted through the sample onto the detector.

32
Q

What does differential interference contrast (DIC) microscopy do?

A

DIC uses an optical system that converts variations in thickness among different parts of the cell into differences in contrast. Kind of gives a sense that the 2D image is 3D.

33
Q

What is fluorescence microscopy?

A

A fluorescent dye is attached to a molecule of interest in fixed or living cells. The dye molecules absorb light at one wavelength and emit light at a different wavelength.

34
Q

What is confocal microscopy?
What is the process of obtaining an image when we use confocal microscopy?

A

It allows images of increases contrast and detail to be obtained by analyzing fluorescence from only a single point in the specimen.
A pinpoint of light is focused on the specimen at a particular depth, and emitted fluorescent light is collected by a detector. Before reaching the detector, the fluorescent light emitted by the specimen must pass through a confocal aperture placed at the point where light emitted from the chosen depth of the specimen comes into focus. As a result, only in-focus light is detected.

34
Q

If light microscopy can only get down 0.2 um, how can we see super small stuff like proteins and RNA?

A

Use fluorescence microscopy and attach fluorescent molecules to the proteins or mRNA and can detect them by the fluorescent microscopy.

35
Q

What is Transmission Electron Microscopy?

A

Magnification about 500,000.
Resolution: 1nm
Operates on the same basic principles as the light microscope but uses electrons instead of light.
Expensive.

36
Q

Why use electrons in TEM?

A

Specimens are fixed and stained with salts of heavy metals, which provide contrast by scattering electrons.

37
Q

Light vs. Electron beam.

A

Wavelength of electrons is much smaller than that of light, which is why they can resolve smaller things.

38
Q

At 1uM resolution with a TEM system, what kind of structures could you see?

A

Cell membrane, mitochondria, nuclei, lysosomes, ER, cytoplasm, for example (may include more)

39
Q

What is Scanning electron microscopy?

A

The surface of the cell is coated with heavy metals. Electrons that are scattered are collected to generate a 3-D image.

40
Q

If you wanted to visualize the movement of individual microtubules during the anaphase stage of mitosis, which microscopy technique would be the best?

A

Confocal microscopy.
If you used transmission, you have to slice and stain, so you won’t see the movement.

41
Q

What are the two types of staining in TEM systems?

A

Positive: heavy metal salts that bind to lipids, proteins, and nucleic acids. Will stain the cell itself, so the cell has dark components and will be against a lighter background.
Negative: Antibodies attached top a heavy metal. Allows us to look at specific molecules. Molecules will be light, and the edge of the molecules will be dark black.

42
Q

What is an excitation filter in fluorescence microscopy?
What is a barrier filter?
What is a dichroic mirror?

A

Only allows wavelength of light that can hit the fluorescent molecule.
Only allows one color in.
Will reflect the wavelength and bounce it down and then will go through.

43
Q

Cells are composed of…?
Cell structure determines…?

A

H20, inorganic ions, and carbon-containing molecules. The structures of these molecules determines all aspects of cell behavior.

44
Q

Carbohydrates include?

A

Simple sugars and polysaccharides.

45
Q

What are Monosaccharides?

A

Monosaccharides are simple sugars and are the major nutrients of the cells. The basic formula is CH2O

46
Q

What provides the principal source of cellular energy?

A

Glucose (C6H12O6)