Chapter 1 Flashcards
1
Q
Differences btw Prokaryotic and Eukaryotic cells (5 each)
A
Prokaryotes have no nucleus , smaller, have no cytoplasmic organelles, contain less base pairs in the DNA, have single circular DNA molecules
Eukaryotic have a nucleus and organelles, bigger, contains more base pairs in DNA, and has multiple linear DNA
2
Q
What the two types of cells ?
A
Prokaryotic and Eukaryotic cells
3
Q
Miller’s experiment 1950 showed_
A
organic molecules could form spontaneously in cnds thought to have existed on early Earth
4
Q
The first living cells arose from_
A
Spontaneous formation of organic molecule probably provided the basic materials
5
Q
What did other experiments show about organic molecules?
A
That they can spontaneously polymerize
6
Q
What was the critical characteristic of the macromolecule from which life evolved?
A
The ability to replicate
7
Q
Altman and Cech(1980) discovered what about RNA?
A
The it can catalyze chemical rxns including polymerization of nucleotides
8
Q
During the RNA world what did they believe RNA had?
A
RNA was/is believed to have been the initial genetic system in evolution
9
Q
RNA can serve as__for its own replication, as well as __rxns
A
template, catalyze
10
Q
What is a gene?
A
Segments of DNA that encode proteins or RNA
The functional units of inheritance
11
Q
What is Transcription?
A
nucleotide gene sequence is copied into RNA
12
Q
What is Translation?
A
nucleotide sequence of RNA is used to specify the order of amino acids in a protein
13
Q
What is are phospholipids?
A
basic components of all present day biological membranes
14
Q
How did the first cell arose?
A
From self-replicating RNA and was enclosed in a phospholipid membrane
15
Q
Characteristic of phospholipids (1)
A
Amphipathic i.e., water-insoluble ( Hydrophobic) hydrocarbon chains are joined to water-soluble (Hydrophilic ) head groups
16
Q
What happens when phospholipids are placed in
water ?
A
They spontaneously aggregate into a bilayer
17
Q
What do cells use as their source of metabolic energy?
A
ATP - adenosine 5’-triphosphate
18
Q
Mechanisms of ATP generation are thought to have evolved in 3 stages_
A
Glycolysis
Photosynthesis
Oxidative metabolism
19
Q
Glycolysis is _
A
Glucose = lactic acid + 2ATP
evolved when Earth’s atmosphere was anaerobic
20
Q
Photosynthesis is_
A
6CO2 + 6H2O = Glucose + 6O2
allowed evolution of oxidative metabolism
21
Q
Oxidative metabolism is _
A
Glucose + 6O2 = 6CO2 + 6H20 + 36-38 ATP
22
Q
Name 3 present day prokaryotes and their characteristic/s
A
Archaebacteria - extreme living cnds
Bacteria - Large grp live in diff environments
Cyanobacteria - most complex and largest. Photosynthesis evolved thru them
23
Q
Archaebacteria
A
extreme living cnds
24
Q
Bacteria
A
Large grp live in diff environments
25
Cyanobacteria
Most complex and largest. Photosynthesis evolved thru them
26
Escherichia coli (E. coli) is_
- Is a prokaryote cell
27
Name 4 characteristics of the E.coli prokaryote cell
- Rigid cell wall of polysaccharides and peptides
- Plasma membrane - wc is a phospholipid bilayer with proteins
- has circular DNA in a nucleoid (wc is not surrounded by a membrane)
- Cytoplasm contains 30K ribosomes (site of protein synthesis)
28
Functions of the nucleus in Eukaryotic cells
contain DNA molecules
| site of DNA replication and RNA synthesis
29
Mitochondria
site of oxidative metabolism
30
Chloroplasts
site of photosynthesis
31
Lysosomes and peroxisomes
metabolic compartments for digestion of macromolecules for oxidative rxns
32
Vacuoles
in plant cells
| digestion of macromolecules and storage of waste products and nutrients
33
Endoplasmic reticulum
- Network of intracellular membranes extending from nuclear membrane thru out the cytoplasm
- process and transport of proteins and lipid synthesis
34
Golgi apparatus
- further processing and sorting of proteins
- lipid synthesis
- in plant cells - synthesis of polysaccharides that compose of cell wall
35
Cytoskeleton
- network of protein filaments extending thru out the cytoplasm
- structural framework
- determines cell shape and organization
- movement of whole cells, organelles, & chromosomes during cell division
36
Endosymbiosis is _
prokaryotic cells living inside the ancestors of eukaryotes
| - Eukaryote organelles are thought to have arisen thru Endosymbiosis
37
Evidence that links prokaryotes to mitochondria and chloroplasts due to Endosymbiosis
- Mitochondria and chloroplasts are similar size to bacteria (size)
- Like bacteria, they reproduce by dividing in two. (reproduction)
- Both contain their own DNA, which encodes some of their components. (DNA)
- The DNA is replicated when the organelle divides; the genes are transcribed within the organelle and translated on organelle ribosomes
- The ribosomes and ribosomal RNAs are more closely related to those of bacteria than to those encoded by the eukaryote nuclear genome. (ribosomal DNA)
38
Mitochondria are thought to have evolved from
aerobic bacteria.
39
Chloroplasts are thought to have evolved from
photosynthetic bacteria, such as cyanobacteria.
40
T/F
| Eukaryotes are either unicellular or multicellular?
T
41
Name two examples of unicellular eukaryotes
ciliated protozoan Paramecium
and
green alga Chlamydomonas
42
The ciliated protozoan Paramecium can be 350 µm long and is specialized for
movement and for feeding on bacteria and yeast.
43
green alga Chlamydomonas, have
chloroplasts, and can carry out photosynthesis
44
multicellular algae, such as Volvox, may represent an evolutionary transition from
single cells to multicellular organisms.
45
Another example of the transition to multicellularity is the _
amoeba Dictyostelium discoideum wc alternates between unicellular and multicellular forms, depending on the availability of food.
46
Plants have three main tissue systems
Ground , Dermal, and Vascular Tissue
47
Ground tissue _
Parenchyma cells—site of metabolic reactions, including photosynthesis.
Collenchyma and sclerenchyma—have thick cell walls and provide structural support.
48
Dermal tissue—
covers the surface of the plant; forms a protective layer and allows absorption of nutrients.
49
Vascular tissue (xylem and phloem)—
elongated cells that transport water and nutrients throughout the plant
50
Animals have five main tissue types:
```
Epithelial cells
Connective tissues
Blood
Nervous tissue
Muscle cells
```
51
Epithelial cells
form sheets that cover the surface of the body and line internal organs.
52
Connective tissues
include bone, cartilage, and adipose tissue. Loose connective tissue is formed by fibroblasts
53
Blood contains several different cell types, such as :
- Red blood cells (erythrocytes) function in oxygen transport.
- White blood cells (granulocytes, monocytes, macrophages, and lymphocytes) function in inflammatory reactions and the immune response
54
Nervous tissue
support cells and nerve cells, or neurons, and various types of sensory cells.
55
Muscle cells are responsible
for the production of force and movement.
56
The simplest eukaryotes is
yeast
57
The fruit fly Drosophila melanogaster
Has a short reproductive cycle (2 weeks) makes it very useful for genetic experiments.
58
mouse-ear cress, Arabidopsis thaliana.
is a model for plant molecular biology and development
59
Resolution—
ability to distinguish objects separated by small distances— is even more important than magnification
60
Fluorescence resonance energy transfer (FRET)
Two proteins are coupled to different fluorescent dyes.
The light emitted by one GFP variant excites the second.
This is used to study interactions between proteins in a cell.
61
image deconvolution.
used to improve the images of fluorescence microscopy
62
In visualizing protein localization within a cell, what are the relative advantages and disadvantages of tagging proteins with green fluorescent protein (GFP) versus using a fluorescent antibody specific to the protein of interest (immunofluorescence)?
The main advantage of using GFP-tagged protein is that fixing, which kills cells & cause artifactual results, is not required. This makes it possible to observe subcellular localization in live cells. The localization of GFP-tagged proteins can be observed in real time in response to various inducers by infusing them into the sample while on the microscope. One potential disadvantage of using GFP-tagged proteins is that the presence of the GFP tag (which has a size of approximately 30 kilodaltons) could alter the structure of the protein and give artifactual results. In fact, that sometimes occurs.
63
Confocal microscopy
increases contrast and detail by analyzing fluorescence from a single point.
64
Which was has a greater resolution, light or electron microscopy?
Electron microscopy
65
Metal shadowing is used to
visualize the surface of subcellular structures or macromolecules.
The specimen is sprayed with a thin layer of metal (such as platinum) from an angle, which results in a shadowing effect.
66
Freeze fracturing:
specimens are frozen in liquid nitrogen and then fractured with a knife blade. A specimen is then shadowed with platinum.
This often splits the lipid bilayer, revealing the interior faces of a cell membrane.
67
Imagine you are studying an inducible transcription factor called X. You make a cellular lysate and carry out a series of centrifugation steps at increasing speeds to localize X. You find that prior to induction, X is in the supernatant after a fourth, very high speed ultracentrifugation step; however, after induction it is found in the pellet after only one, relatively low speed ultracentrifugation step. What might this tell you about how X is regulated? What other techniques might you carry out to confirm your results?
This indicates that X is present in the cytoplasm before induction and localises to the nucleus upon induction to carry out the transcription of its target genes. Reason: ultracentrifugation is a process of applying various able magnitudes
This indicates that X is present in the cytoplasm before induction and localises to the nucleus upon induction to carry out the transcription of its target genes.
Reason: ultracentrifugation is a process of applying various able magnitudes of centrifugal force (here, to the lysed cells) – the centrifugation force increases each time the lysate undergoes centrifugation. The heavier components of the cells will pellet down at lower speeds owing to their higher molecular weight while the light one will require comparatively higher speeds to sediment/ pellet out. Following is the general order in which the cell component pellet out:-
> Nucleus
> Most other organelles like mitochondria, peroxisomes, chloroplasts, etc
> Microsomes ( disrupted vesicles of the endoplasmic reticulum)
> Cytoplasmic components
An immunostaining of the cells using antibody specific for factor X, before and after induction, and help you confirm its localisation in the 2 cases.
Also an EMSA, if the target genes for X are known would help. Binding to DNA would be observed in case of induction of while the no binding would be observed when not induced. But this is not confirmation of its localises in the cytoplasm.
68
Scanning electron microscopy provides
a 3-D image of cells.
69
Super-resolution light microscopy
increases resolution of fluorescence microscopy to 10–100 nm.
70
Subcellular fractionation
In order to determine the function of organelles, they must be isolated from the cell.
71
Differential centrifugation was developed in the 1940s and 1950s is used to
separate cell components on the basis of size and density.
72
Density-gradient centrifugation—
organelles are separated by sedimentation through a gradient of a dense substance, such as sucrose.
73
Velocity centrifugation—
starting material is layered on top of the sucrose gradient. Particles of different sizes sediment through the gradient at different rates.
74
Equilibrium centrifugation in density gradients separates
subcellular components on the basis of their buoyant density.
The sample particles are centrifuged until they reach an equilibrium position at which their buoyant density is equal to that of the surrounding sucrose or cesium chloride solution
75
Callus
a mass of undifferentiated cells
76
Viruses are
- intracellular parasites that cannot replicate on their own.
77
How do viruses reproduce ?
- They reproduce by infecting host cells and usurping the cellular machinery to produce more virus particles.
78
T/F
| Viruses consist of DNA or RNA surrounded by a protein coat.
T
79
What are bacteriophage?
Bacterial viruses (bacteriophages) have simplified the study of bacterial genetics.
-Bacterial viruses are extremely useful experimental systems for molecular genetics and have led to understanding of many fundamental principles.
80
retroviruses have RNA genomes but synthesize a
DNA copy of their genome in infected cells.
81
The feature that most clearly separates eukaryotes from prokaryotes is the presence of _______ in eukaryotic cells
nucleus
83
Totipotency is a term that is often applied to cells in a plant callus tissue in culture and might by extension be applied to embryonic stem cells from animals. With appropriate manipulation of nutrients and growth regulatory molecules, an entire plant can be regenerated from a single cell within a callus. Taking this as an example of the developmental potential of a single plant cell, define the term "totipotency."
the ability of a single cell to divide and produce all the differentiated cells in an organism,
84
The original cell was thought to have arisen from the enclosure of self-replicating _______ by a phospholipid membrane.
rna
85
The source of the atmospheric oxygen necessary for the development of oxidative metabolism is thought to have been
photosynthesis
86
The original atmosphere of Earth is thought to have been rich in
CO2, N2, H2, H2S, and CO.
87
Chloroplasts are thought to have originated from endosymbiosis of _______ by a large host cell.
photosynthetic eubacteria such as cyanobacteria
88
The genome of eukaryotes consists of genes derived from
both archaebacteria and bacteria.
Individual eukaryotic genes appear to have originated from either archaebacteria or bacteria, with basic cellular metabolism genes typically coming from eubacteria. Hence, the eukaryotic genome is a mosaic with respect to its origin.
89
Which of these organisms is not a unicellular eukaryote?
Question 7 options:
Saccharomyces cerevisiae
Paramecium
Methanococcus
Chlamydomonas
Methanococcus and archaebacteria
These are unicellular
Chlamydomonas
Saccharomyces cerevisiae
Paramecium
90
Transmission electron microscopy is used to-
A. study in single, thin sections the shapes of whole cells.
B. view living cells in three dimensions.
C. observe subcellular organelles and macromolecules.
D. view fluorescently labeled proteins in cells.
C. observe sub-cellular organelles and macromolecule
With the use of salts and heavy metals to provide contrast, the electron microscope can be used to visualize subcellular structures in some detail.
91
```
How many genes does an E. coli have?
A 4,300
B 6,000
C 14,000
D 20,000-25,000
```
4300
92
```
Which of the following is a high-resolution light microscope technique for detecting interactions between proteins?
(A) FRAP (fluorescence
recovery after
photobleaching)
(B) FRET (fluorescence
resonance energy
transfer)
(C) MPEM (multi-photon
excitation microscopy)
(D) Confocal microscopy
```
(B) FRET (fluorescence
resonance energy transfer)
A FRET signal requires that individual fluorescent dyes carried by two separate proteins be close together in a complex. Energy transfer between fluorescent dyes is efficient only when the two fluorescent dyes are brought close together.
93
```
An E. coli cell under well-defined laboratory conditions divides about every
(A) 20 minutes.
(B) 2 hours.
(C) 12 hours.
(D) 24 hours.
```
(A) 20 minutes.
On rich laboratory medium, a typical E. coli cell will divide every 20 minutes.
94
```
In fluorescence microscopy, the immediate source of the light detected is light that has been _______ the sample.
(A) absorbed by
(B) emitted by
(C) exciting
(D) scattered from
```
(B) emitted by
The light detected is emitted by the sample. In fluorescence, the excitation light is absorbed by the fluorescent group (electrons excited to a higher energy level), and light is then emitted as the electrons fall back to their basal energy level.
95
```
Which of the following are the most commonly used mammals for genetic studies?
(A) Humans
(B) Xenopus laevis
(C) Mice
(D) Cats
```
C) Mice
Although not as easily manipulated genetically as organisms such as C. elegans and D. melanogaster, mice are the most commonly used mammals for genetic studies.
96
Embryonic stem cells are different from primary cell cultures or permanent cell lines derived from a tissue in that they are capable of
Generating many cell types
97
In contrast to yeast or bacterial cells, animal cell cultures are grown on fairly complex media, with added amino acids, vitamins, and/or hormones. This is primarily because animal cells
typically live in association with other cells.
are less capable of transporting small molecules across their membranes.
come from organisms that have specialized cell types.
have too many genes to be able to keep track of the biosynthesis of needed metabolites.
(A) come from organisms that have specialized cell types.
Because of cell specialization and, as part of this, the existence of a circulatory system, animal cells can be specialized and derive nutrients from diet and vitamins and derive hormones from other cell types.
98
Approximately how many doublings can normal human fibroblasts undergo in culture?
(B) 50 to 100
After 50 to 100 doublings, the cells will stop growing and die.
99
The Rous sarcoma virus (RSV) is
a strain of virus that causes neurodegeneration in chickens.
100
What is the theoretical diffraction limit of resolution of a light microscope used to look at a sample through oil?
0.22
101
In fluorescence microscopy, the immediate source of the light detected is light that has been _______ the sample.
Question 17 options:
absorbed by
emitted by
exciting
scattered from
(B) emitted by
The light detected is emitted by the sample. In fluorescence, the excitation light is absorbed by the fluorescent group (electrons excited to a higher energy level), and light is then emitted as the electrons fall back to their basal energy level.
102
Which of the following is a high-resolution light microscope technique for detecting interactions between proteins?
Question 18 options:
FRAP (fluorescence recovery after photobleaching)
FRET (fluorescence resonance energy transfer)
MPEM (multi-photon excitation microscopy)
Confocal microscopy
(B) FRET (fluorescence
resonance energy transfer)
A FRET signal requires that individual fluorescent dyes carried by two separate proteins be close together in a complex. Energy transfer between fluorescent dyes is efficient only when the two fluorescent dyes are brought close together.
103
Transmission electron microscopy is used to
Question 19 options:
study the shapes of whole cells in single, thin sections.
view living cells in three dimensions.
view fluorescently labeled proteins in cells.
observe subcellular organelles and macromolecules
(A) observe subcellular organelles and macromolecules.
With the use of salts and heavy metals to provide contrast, the electron microscope can be used to visualize subcellular structures in some detail.
104
What is the smallest number of ultracentrifugation steps necessary to separate nuclei from ribosomes in a cellular lysate?
1
105
Why is RNA thought to have arisen on Earth prior to proteins and DNA?
Self-Copying RNA. The RNA world hypothesis suggests that life on Earth began with a simple RNA molecule that could copy itself.
the original cell was thought to have arisen from the enclosure of self-replicating rna by a phospholipid membrane.
106
Why must the development of photosynthesis have preceded the development of oxidative phosphorylation?
Photosynthesis allowed some cells to harness energy from sunlight; they no longer needed preformed organic molecules. The first photosynthetic bacteria used H 2 S to convert CO 2 to organic molecules a pathway still used by some bacteria.
106
Mitochondria and chloroplasts are both thought to have become organelles within eukaryotic cells through endocytosis. Mitochondria are thought to have evolved from aerobic eubacteria, while chloroplasts can be readily related to cyanobacteria. What present-day traits of these organelles provide evidence of these origins?
A free-living organism has its own DNA that can be transcribed and translated into proteins within the organism. Both mitochondria and chloroplasts contain their own DNA genome that is transcribed within the organelle into RNA and translated therein into proteins. The ribosomes and proteins made can be related by their size and sequence to present-day aerobic bacteria and cyanobacteria, respectively.
107
How good an indicator is DNA content of the cellular complexity of an organism? Give examples to explain your answer.
There is no correlation between DNA content and the complexity of an organism. This is known as C-value paradox refers to the observation that genome size does not uniformly increase with respect to perceived complexity of organisms.
Chromosome number is not correlate to the complexity of an org. Eg humans have 46 chromosomes and ducks have 80 chromosomes, even tho ducks have more human are more complex than them
size of chromosome is more related to complexity of individual ie larger chromosomes contain more genes
If there are more genes that contain coding or instruction for a particular trait then an org is more complex
108
Why have viruses been so useful in the elucidation of cellular processes?
Because they use the host cellular machinery to propagate themselves, they have been used to study bacterial cell biology. For example, bacteriophage T4 was used extensively in early molecular genetic studies.
Many viruses inhibit the synthesis of host cell macromolecules, including DNA, RNA, and protein. Viruses may also change cellular transcriptional activity, and protein-protein interactions, promoting efficient production of progeny virus.
109
Microscopy, be it light or electron microscopy, is a major research tool in the molecular approach to the study of the cell. What does this tell us about the level of resolution needed to solve many problems in cell biology?
Microscopy provides a good indication of the scale at which cell biology attempts to answer questions about cell structure and function. These include questions at the subcellular level, cellular level, and tissue level. At the subcellular level, genes or protein machines must be understood. At the tissue to organism level, processes as complicated as nerve function and memory are a goal for our understanding. For example, much of protein localization work in cells is done within the 0.22 μm limit of light microscopy.
110
How similar are the nutritional requirements for the culture of HeLa cells to those of a human?
Basal media for the cultivation of HeLa cells, a cell line of human origin, provides the essential amino acids that the cell cannot synthesize: vitamins, salts, glucose, and a range of polypeptide hormones for which serum is the source. With the exception of glucose as an energy source, these small molecules or inorganic nutrients are substances that neither the HeLa cells nor a human can synthesize. In the case of the polypeptide hormones, other cell types in the human body can synthesize them, and they are carried by the blood stream to other cells. Hence, for HeLa cells, what must be supplied is greater than what must be ingested in the human diet.
111
2 types of cell cultures
Primary cell lines: cells straight from the tissue with no passage. Because it is straight from the tissue it is a heterogenous mixture of cell types, but they're in their physiological conditions.
Cell lines: have at least one pass (usually 50-60 times). Cell population becomes more homogenous -- immortalized cell lines, usually tumors or cancel cells.
These are "modified" cell lines are not in their physiological conditions.
112
HeLa cells
Cancer cell line for biomedical purposes.
113
Techniques to study cells
Microscopy
Subcellular fractionation
-- velocity centrifugation (density gradient)
114
How to visualize proteins in cells
Antibodies (about 3 months & expensive)
| GFP tagged proteins (quicker & cheaper)
115
GFP Tagged Protein
GFP-A fused protein to GFP tag.
Transfection.
Sometimes GFP disrupts protein localization.
From jellyfish. Can be fused to any protein of interest using standards methods of recombinant DNA, and the GFP-tagged protein can then be expressed in cells & detected by fluorescence microscopy, without the need to fix and stain the cell as would be required for the detection of proteins with antibodies.
116
Fluorescence Microscopy
Advantage is INCREASED SENSITIVITY.
Selective staining of different components.
How are molecules visualized?
- Dyes that bind to particular structures or molecules.
- Dyes coupled to antibodies (immunofluorescence).
- Fluorescent protein tags (GFP and variants).
Allows us to see distribution of a specific molecule.
Has two filters -- before light reaches the specimen - to excite the dye and filter that illuminates light (emits longer wavelengths - less energy).
117
Confocal Microscopy
Contrast is even better than light microscopy because it can focus on thinner tissues & put the images together to form 3D picture.
118
Electron Microscopy
Higher resolution than light microscopy. Used to resolve the fine structure of the cell.
Two types: Transmission EM and Scanning EM.
119
Transmission Electron Microscopy
Transmits a beam of electrons THROUGH the sample.
| Generates a 2D image.
120
Scanning Electron Microscopy (SEM)
Electrons scattered to look at the surface details of a specimen (specimen is coated with metal that reflect electrons to produce the image). Produces a 3D image
