02 Cell and Molecular Biology Flashcards
1
Q
Name the 5 characteristics common to all cells
A
- they arise from pre-existing cells
- genetic information is stored in DNA in chromosomes
- proteins are synthesized on ribosomes
- a selectively permeable plasma membrane encloses every cell
- sub-cellular components are suspended in a semifluid substance called cytosol
2
Q
1 mm is how many micrometres μm
A
1000 μm
3
Q
how many nanometres are there in 1 μm
A
1000
4
Q
What electron microscopy must be used to view protein and lipid structures?
A
Electron microscopy
5
Q
What electron microscopy must be used to view most plant and animal cells?
A
Light microscopy
6
Q
What electron microscopy must be used to view mitochondria?
A
Light microscopy
7
Q
What electron microscopy must be used to view viruses and ribosomes ?
A
Electron microscopy or super resolution microscopy (light)
8
Q
What are the three parameters of microscopy?
A
magnification, resolution, contrast
9
Q
What is magnification?
A
enlargement of an image
10
Q
What is resolution?
A
a measure of the clarity of an image
11
Q
What is contrast?
A
the difference in brightness between light and dark areas of an image
12
Q
What are the two subdivisions of electron microscopy?
A
Scanning electron microscope (SEM)
Transmission electron microscope (TEM)
13
Q
What is light microscopy used for?
A
used to visualise whole cells and large sub-cellular organelles
14
Q
What is Electron microscopy used for?
A
Instead of lights, EM’s use electromagnets to focus a beam of light through the specimen (TEM) or onto its surface (SEM)
15
Q
Describe the difference between TEM and SEM
A
resolution
- TEM, 2nm
- SEM, 10 nm
used for:
- TEM, study internal cell structure eg organelles, proteins, nucleic acids
- SEM, study cell surface and generate 3D images
beam focus:
- TEM focus beam of electrons through the specimen
- SEM focus beam of electrons on surface of specimen
16
Q
What is the purpose of cell fractionation ?
A
Isolates cell components based on size and density
17
Q
How can cells be separated using cell fractionation ?
A
blender to break the membrane - forms homogenate - centrifuged
larger organelles will deposit at the bottom at a lower centrifugation force, smaller organelles will require larger centrifugation force to deposit at the bottom
18
Q
List the 8 components of prokaryotic cells
A
- nucleoid - DNA concentrated here but not enclosed by membrane
- little or no structure or organelles
- ribosomes - synthesise proteins
- plasma membrane - encloses cytoplasm
- cell wall - rigid structure
- glycocalyx - outer coating consisting of a capsule or slime layer
- fimbria - attachment to other bacteria
- flagella - locomotion
19
Q
What structures do plant cells have that animal cells lack? Explain their function.
A
cellulose cell wall - protects cell and maintains shape
central vacuole - storage and breakdown of waste products
chloroplasts - photosynthetic organelle
20
Q
State what the defining feature is of eukaryotic cells
A
have a membrane bound nucleus which contains most of the cell’s DNA
21
Q
_____ are surface appendages that allow a bacterium to stick to a surface.
A
Fimbria
22
Q
What is a function of a bacterium’s capsule?
A
protection
23
Q
Where is a bacterial cell’s DNA found?
A
nucleoid region
24
Q
Which organelle carries out cellular respiration?
A
mitochondrion
25
What is the function of mitochondria?
Mitochondria convert the chemical energy of organic molecules to chemical energy in the form of ATP.
26
What is the name given to the double membrane that encloses the nucleus?
nuclear envelope
27
The _____ is composed of DNA and protein.
chromatin
28
Ribosomal subunits are manufactured by the _____.
nucleolus
29
_____ are the sites of protein synthesis.
ribosomes
30
Which organelle manufactures proteins bound for secretion out of the cell?
rough endoplasmic reticulum
31
briefly describe the process of protein synthesis on a rough er ribosome to a golgi.
The ribosomes associated with the rough ER synthesize secretory proteins bound for the exterior of the cell. Further processing and packaging occurs in the Golgi apparatus.
32
Where is calcium stored?
smooth endoplasmic reticulum
33
What roles does the smooth ER have?
- storing calcium
- role in detoxification and lipid synthesis
34
What is a hollow rod that shapes and support the cell?
microtubules
35
_____ is/are identical in structure to centrioles.
basal bodies
36
What organelle produces H2O2 as a by-product?
peroxisome
37
What is the role of the central vacuole
regulates cytoplasm composition, creates internal pressure and stores cell compounds
38
What is the function of chloroplasts?
makes sugar by converting light energy into chemical energy
39
What do the photosynthetic reactions do?
converting solar energy into chemical energy
40
Where is rubisco found?
stroma (chloroplasts)
41
Where is photosystem 1 found?
internal membrane of mitochondrion and/or chloroplast
42
Where is isocitrate dehydrogenase found?
matrix (mitochondrion)
43
Where is phosphofructokinase found in the cell?
cytoplasm
44
What is an example of a motor protein? What is its function?
actin - move along protein tracks, responsible for moving vesicles and organelles within the cell
45
What is an integral protein?
spans across the membrane (transmembrane)
46
What components pass through the nuclear pore during normal cellular activity?
ribosomal subunits and mRNA
47
What constitutes the endomembrane system?
nucleus, endoplasmic reticulum, golgi apparatus, lysosomes
48
What is the function of the nucleolus?
synthesis of rRNA
49
What constitutes chromatin?
DNA wrapped around 8 histone proteins
50
What is the nuclear envelope comprised of?
2 phospholipid membrane layers
51
What is the function of the endoplasmic reticulum?
smooth ER - synthesis of phospholipids
rough ER - studded with ribosomes for protein synthesis
52
What structure is continuous with the nuclear envelope?
rough ER
53
Describe the orientation of the Golgi in terms of cis and trans
cis closest to rough ER, trans closest to plasma membrane
54
Explain the process of the Golgi modifying proteins
1. vesicle moves from ER to golgi
2. Vesicles coalesce to form new cis golgi cisternae
3. Cisternal maturation, Golgi cisternae move in a cis-to-trans direction
4. Vesicles form and leave Golgi, carrying specific proteins to other locations or to the plasma membrane for secretion
5. Vesicles transport specific proteins backwards to newer Golgi cisternae
6. Vesicles also transport proteins back to ER
55
Where are lysosomes synthesized?
Golgi apparatus
56
Describe the process of phagocytosis
1. lysosome contains active hydrolytic enzymes
2. food vacuole fuses with lysosome
3. hydrolytic enzymes digest food particles
57
Describe the process of Autophagy
1. Lysosome fuses with vesicle containing damaged organelles
2. Hydrolytic enzymes digest organelle components
58
What is the stroma of a chloroplast analogous to?
cytosol
59
What are the three functions of the cytoskeleton?
maintain cell shape
facilitates cell movement
facilitates movements of components within the cell
60
What are the three types of cytoskeletal filaments?
microtubules, microfilaments, intermediate filaments
61
What are microtubules comprised of ? Describe its function.
tubulin
- maintains cell shape,
- cell motility (cilia flagella)
- chromosome movements in cell division
- organelle movements
62
What are Microfilaments comprised of ? Describe its function.
Actin
- maintain cell shape
- changes in cell shape
- cell motility (pseudopodia)
- cell division
63
What are Intermediate filaments comprised of ? Describe its function.
fibrous proteins supercoiled into thicker cables
eg. keratin
- maintain cell shape
- anchorage of nucleus and other organelles
- formation of nuclear lamina
64
What structure provides a network for vesicles to move along inside a cell?
microtubules
65
How do microtubules contribute to the function of cilia and flagella?
microtubules enable bending of the structure as the motor proteins (dyneins) can walk along the tubule
66
Describe the structure of a basal body in the cilia
triplets anchored to a central microtubule by cross linking proteins. Motor proteins on the outer triplet microtubule structures
67
How thick is the phospholipid bilayer?
7-8 nm
68
Describe the structure of a phospholipid
2 fatty acid tails
glycerol head bound to a phosphate group
69
Where is the ECM found
only in animal cells in the extracellular side of membrane
70
What is the ECM analogous to in plant cells?
cell wall
71
What is fibronectin
protein that links a membrane protein to the ECM
72
How is membrane fluidity maintained?
1. unsaturated phospholipid fatty acid tails - kinks
2. cholesterol - fluidity buffer, at cold temperatures when fatty acid tails go stiff, it creates space
73
List the 6 examples of membrane protein functions and give an example of each
- enzymatic activity eg. cristae membranes, catalytic activity
- signal transduction eg. receptor molecule in membrane - signalling cascase
- cell-cell recognition eg. receptor recognizing other proteins - communication
- attachment to the cytoskeleton and ECM eg. fibronectin, maintain cell shape
- intercellular joining (cell junctions) eg. communication, adhering
- transport eg. diffusion
74
Describe how the synthesis of membrane components occurs and the orientation of these molecules throughout the process.
1. synthesis of phospholipid in the ER - transmembrane protein attached facing into lumen
2. throughout golgi modification and packaging, orientation remains the same
3. fuses with the plasma membrane and the transmembrane protein now faces into ECM (if orientation was the other way around in ER, protein would face the incorrect way in PM - cant function)
75
List the cell junctions in animal tissues
tight junctions
desmosomes
gap junctions
76
State the cell junctions in plant cells
plasmodesmata
77
Describe the composition of tight junctions
claudins and occludins - prevent fluid from moving across a layer of cells
78
Describe the composition of desmosomes
intermediate filaments, keratin
linking protein, cadherin
provides adhesion between cells
79
Describe the composition of Gap junctions
6 connexins, ions, AA from one cell to another
cytoplasm of two cells continuous
80
What are plasmodesmata analogous to? Where can they be found?
gap junctions between the cell walls of plant cells
81
How do membranes regulate molecular traffic? Give examples
passive transport - diffusion, facilitated diffusion
active transport - Na/K pump
82
Describe what is meant by passive transport
molecules move passively from high to low concentrations
spontaneous
83
Explain diffusion
small, non-polar molecules like oxygen and CO2 and lipids are hydrophobic and can easily diffuse through the cell membrane
84
Explain facilitated diffusion
Polar molecules like water ions and glucose are hydrophilic and require TRANSPORT PROTEINS to diffuse through the membrane
85
What is osmosis
diffusion of water across membrane
86
What are the two mechanisms for facilitated diffusion
a channel protein and a carrier protein
87
Describe what is meant by active membrane transport
molecules move across membrane against concentration gradient
usually require energy in the form of ATP
all carrier proteins
88
Describe the benefits of membrane transport proteins
provide selectivity
can increase rate of transport
continuously recycled
BUT
rate of transport limited by number of proteins
89
Describe the mechanism of the NA/K pump
1. 3 Na+ bind to carrier protein
2. carrier protein is phosphorylated - binding of phosphorus induces shape change of Na+ binding site = decreased affinity and Na+ released into extracellular fluid
3. 2 K+ bind causing dephosphorylation
4. Change in shape of K+ binding site and higher affinity again for Na+
90
How are large molecules transported?
exocytosis and endocytosis.
91
Name the three types of endocytosis
phagocytosis "cell eating" - fuse with lysosome
pinocytosis "cell drinking" - not selective, vesicles form
receptor mediated endocytosis - highly selective, ligand binding, cluster, cell enveloped them, vesicle
92
What is the highest energy form of adenosine?
Adenosine triphosphate (ATP) is the high-energy form of adenosine because it contains the most phosphate groups (three).
93
Which part of the adenosine triphosphate molecule is released when it is hydrolyzed to provide energy for biological reactions?
The γ -phosphate is the primary phosphate group on the ATP molecule that is hydrolyzed when energy is needed to drive anabolic reactions. Located the farthest from the ribose sugar, it has a higher energy than either the α - or β -phosphate.
94
What type of reaction breaks the bonds that join the phosphate groups in an ATP molecule?
hydrolysis
95
"Conservation of energy" refers to the fact that _____.
energy cannot be created or destroyed but can be converted from one form to another
96
Chemical energy is a form of _____ energy.
potential
97
In your body, what process converts the chemical energy found in glucose into the chemical energy found in ATP?
cellular respiration
98
What are the by products of cellular respiration
heat, carbon dioxide and water
99
Which of these cell junctions form a barrier to the passage of materials?
tight junctions
100
The primary role of _____ is to bind animal cells together.
desmosomes
101
_____ aid in the coordination of the activities of adjacent animal cells.
gap junctions
102
When molecules move down their concentration gradient, they move from where they are ____ to where they are ___.
Diffusion across a biological membrane is called _____
more concentrated, less concentrated, passive transport
103
Facilitated diffusion is a type of _______.
passive transport
104
Endocytosis moves materials _____ a cell via _____.
into, membranous vesicles
105
You can recognize the process of pinocytosis when _____.
the cell is engulfing extracellular fluid
106
A white blood cell engulfing a bacterium is an example of _____.
phagocytosis
107
___ structure is achieved when a protein folds into a compact, three-dimensional shape stabilized by interactions between side-chain R groups of amino acids.
tertiary
108
___ structure is the result of two or more protein subunits assembling to form a larger, biologically active protein complex.
quaternary
109
___ structure is the sequence of amino acids in a protein.
primary
110
___ structure describes the alpha-helices and beta-sheets that are formed by hydrogen bonding between backbone atoms located near each other in the polypeptide chain.
secondary
111
Proteins are polymers of _____.
amino acids
112
What type of bond joins the monomers in a protein's primary structure?
peptide
113
The secondary structure of a protein results from _____ between repetitive regions of the backbone.
hydrogen bonds
114
Tertiary structure is NOT directly dependent on _____.
peptide bonds
115
When two amino acid monomers are positioned so that the carboxyl group of one is adjacent to the amino group of the other, they can be joined through a ___ reaction. This reaction forms a(n) ___ bond.
dehydration, peptide
116
When would you use a space filling model?
If you wanted to show the 3-dimensional shape of a protein, including all of the atoms composing it
117
When would you use a simplified diagram
If you wanted to show the general shape of a protein, along with some important functional details such as folds and coils
118
When would you use a ribbon model
If you wanted to show the 3-dimensional shape of a protein, including the backbone structure, folds, and coils
119
When would you use a simple shape diagram?
If you wanted to show a generalized protein in which the focus is on the protein's function rather than its structure
120
When would you use a wireframe model?
If you wanted to show the 3-dimensional shape of a protein by showing the amino acid side chains and their interactions
121
What could happen if a mutation in a gene caused a hydrophobic amino acid in a polypeptide to be replaced by a hydrophilic amino acid?
The new amino acid would not form the same interactions with hydrophobic R groups, and the protein's shape would likely be affected.
122
What is the name of the central carbon in an amino acid?
𝛼 carbon
123
List the 4 components of an amino acid
carboxyl, amino, R group and hydrogen
124
What form is the amino acid in at pH 7
ionised state (NH3 + and COOH-)
125
State the three classes of amino acids
Nonpolar - hydrophobic
Polar - hydrophilic
Electrically charges - hydrophilic
126
How are amino acids joined together?
Peptide bonds - carboxyl group to amino group, remove H2O
127
What constitutes a peptide bond?
O=C-N-H
128
What type of reaction forms a peptide bond?
dehydration
129
Are peptide bonds formed simultaneously?
No - one at a time
130
What constitutes the repetitive backbone?
everything but R group
131
What does the R group determine?
sequence/properties determines folding and function
132
Where is mRNA produced?
nucleus
133
What happens to mRNA once it is made it in the nucleus?
Leaves the nucleus through a nuclear pore to the cytoplasm
134
What happens to the mRNA in the cytoplasm?
it attaches to a ribosome and is translated into a protein
135
How often does hydrogen bonding occur between amino acids in the secondary alpha helix structure?
every 4 amino acids
136
Where is the N and C terminus found respectively in an alpha helical membrane protien?
N-terminus in extracellular fluid
C-terminus in cytoplasmic side
137
How do beta pleated sheets form hydrogen bonds?
between the O and H of neighbouring polypeptide backbones
138
What types of side chain interactions are there?
weak interactions
- hydrogen
- ionic bond
- hydrophobic interactions and van der waals
- disulfide bridges (only bw cysteine)
139
Give an example of a quaternary protein
collagen - ECM fibres, 3 coiled, identical
140
Give an example of a quaternary protein
collagen - ECM fibres, 3 coiled, identical
141
What is the function of a chaperone?
assist the folding of proteins
- protects polypeptide from degradation
- polypeptide folds spontaneously into proteins
check correct folding
- refold
- mark for destruction
142
Explain how a chaperone functions
1. unfolded polypeptide enters the cylinder from one end
2. cap attaches causing cylinder to change shape in a way that it creates a hydrophilic environment for the folding polypeptide
3. cap comes off and the properly folded protein is released
143
Explain what is meant by denaturation of a protein
destruction of the 2°, 3° and 4° structure (3D shape)
144
What factors cause a protein to denature?
heat, pH, reducing agents, organic solvents, detergents
145
how does pH affect denaturation?
changes ionisation patterns of R groups
146
how does heat affect denaturation?
break weak bonds
147
how do reducing agents affect denaturation?
reduce S-S bonds to SH
148
how do organic solvents affect denaturation?
disturb hydrophobic and hydrophilic interactions
149
how do detergents affect denaturation?
disrupt hydrophobic interactions
150
What is meant by the hydrolysis of a polypeptide?
addition of H2O to break the polypeptide bond
151
What is a key difference between denaturation oand hydrolysis?
denaturation is the loss of 3D structure (2, 3, 4)
hydrolysis breaks the 1 structure
