Midterm Flashcards
(475 cards)
1
Q
Cell theory
A
cells are the basic unit of structure in all living things
2
Q
Who first named the cell in 1665?
A
Robert Hooke
3
Q
What did Hooke see?
A
Non-living cells from a cork
4
Q
Who first witnessed a live cell under a microscope in 1674?
A
Anton Van Leeuwenhoek
5
Q
Who first developed the cell theory in 1839?
A
Matthias Jakob Schleiden and Theodor Schwann
6
Q
What does the cell theory state?
A
all organisms are composed of one ore more cells, all cells come from pre-existing cells, vital functions occur within cells, contain hereditary information
7
Q
Exceptions to the cell theory
A
viruses are considered by some to be alive (not made up of cells), the first cell did not originate from a pre-existing cell
8
Q
Conditions on Earth (evolution of cells)
A
little oxygen in the atmosphere, thought the environment was rich in hydrogen, methane, and ammonia
9
Q
What did Stanley Miller demonstrate in the 1950’s?
A
the spontaneous formation of organic molecules
10
Q
What was a critical characteristic of self-replication of RNA?
A
the ability to replicate itself
11
Q
What was the discovery made from by Sid Altman and Tom Cech in the 1980’s?
A
the discovery of the ability of RNA to catalyze chemical reactions
12
Q
What is unique about RNA?
A
it can serve as a template for and catalyze its own replication
13
Q
What was RNA world?
A
though to have been an early stage of chemical evolution based on self-replicating RNA molecules
14
Q
What were the first cellular life forms on Earth?
A
Proteinoid-based protocells enclosing RNA molecules
15
Q
What do amphipathic molecules consist of and what does it form?
A
one portion that is soluble in water and another portion that is not. forms a stable barrier between interior of cells and external environment
16
Q
What is glycolosis?
A
an anaerobic breakdown of glucose to lactic acid and occurs in the cytoplasm
17
Q
What does photosynthesis allow the cell to do?
A
harness energy from sunlight
18
Q
What is oxidative metabolism?
A
the principal source of energy for most present-day cells and utilizes highly reactive O2 to generate energy from organic moelcules
19
Q
What do prokaryotes lack and what do eukaryotes have?
A
lack a nuclear envelope and have a nucleus in which the genetic material is separated from the cytoplasm
20
Q
E. Coli is…
A
a prokaryotic cell and a common inhabitant of the human intestinal tract
21
Q
What is E Coli surrounded by?
A
a rigid cell wall that is composed of polysaccharides and peptides (wall is porous and allows passage of molecules)
22
Q
What is beneath E. Coli?
A
a plasma membrane that consists of a bilayer of phospholipids and associated proteins
23
Q
DNA of E. Coli is a single circular molecule that resides in..
A
the organisms nucleoid
24
Q
The mitochondria is the site of…
A
oxidative metabolism
25
Where are chloroplasts found and is the site of?
in the cells of plants and green algae and site of photosynthesis
26
What do lysosomes provide?
specialized metabolic compartments for the digestion of macromolecules
27
What do peroxisomes perform?
various oxidative reactions
28
What do vacuoles perform?
a variety of functions, including the digestion of macromolecules and the storage of both waste products and nutrients
29
What is the ER a network of?
intracellular membranes that functions not only in processing and transport of proteins, but also in the synthesis of lipids
30
What does the Golgi apparatus do?
sorts and transports proteins destined for secretion- site of lipid synthesis, (in plant cells- the site of synthesis of some of the polysaccharides that compose the cell wall)
31
The cytoskeleton is another level of internal organization. What does it provide?
the structural framework of the cell and is responsible for the movements of the entire cells- intracellular transport and positioning of organelles and other structures
32
What is endosymbiosis?
one cell living inside another
33
What does the endosymbiotic theory concern?
the origins of the mitochondria and chloroplasts
34
What does the endosymbiotic theory postulate?
the mitochondria evolved from aerobic bacteria living within their host cell and chloroplasts evolved from endosymbiotic photosynthetic cyanobacteria
35
What is Saccharomyces Cerevisiae?
commonly studied yeasts
36
What are Pseudopodia?
cytoplasmic extensions used for moving and engulfing other organisms- includes bacteria and yeasts
37
What is volvox?
a unicellular green alga and associates with other alga cells to form multicellular colonies (precursors of plants)
38
Yeast mutants have been important in...
understanding many fundamental processes in eukaryotes, including DNA replication, transcription, RNA processing, protein sorting, and the regulation of cell division.
39
Genetic analysis of Drosophila uncovered..
many genes that control development and differentiation, especially with respects to formation of body planes and multicellular organisms
40
Why is the frog an important model for studies of early vertebrate development?
its eggs develop outside the mother and all stages of development from egg to tadpole can be studied in the lab
41
Why are mice most useful for genetic analysis?
many mutations affecting mouse development have been identified -the development of genetically-engineered mice in which specific mutant genes have been introduced into the mouse germ cells, allowing the functions of these genes to be studied in the context of whole animals
42
What are viruses helpful in?
cellular research and human therapies
43
How to viruses work?
cannot replicate on their own-heed to hijack the replication machinery of a host organism- viral DNA or RNA is enclosed in a capsid protein coat
44
Anton Van Leeuwenhoek invented what in the 1670's?
a microscope that magnified objects up to 300 times their size and was able to identify a variety of different cells
45
What does optical resolution decribe?
the ability of an imaging system to resolve detail in the object that is being imaged
46
What does resolution describe?
the ability of a microscope to distinguish objects separated by small distances
47
Bright-field microscopy
light passes through directly through the cell-used to study various aspects of cell structure because of its simplicity (cells are stained with dyes to enhance contrast)
48
Phase-Contrast Microscopy and DIC
use optical systems that convert variations in density or thickness between different parts of the cell to differences in contrast that can be seen in the final image
49
Fluorescence Microscopy
widely used and sensitive for studying the intracellular distribution of molecules
50
Fluorescent Microscope
light microscope used to study properties of organic/inorganic substances using the phenomena of fluorescence
51
Steps for fluorescent microscope
specimen is labeled with a fluorescent molecule called a fluorophore-then specimen is illuminated with light of a specific wavelength which is absorbed by the fluorophores, causing them to emit longer wavelengths of light
52
What is the green fluorescent protein (GFP) used for?
to visualize proteins within living cells
53
Fluorescence recovery after photobleaching (FRAP) is used to study
the movements of GFP-labeled proteins
54
Fluorescence resonance energy transfer (FRET) is used to study
the interactions of two proteins with one another within a cell - two GFP variants are used: the light emitted by one GFP excites the second- if the molecules interact (brought close), the first GFP will excite the second resulting in emission of the second GFP
55
Confocal Laser Scanning Microscopy
a technique for obtaining high-resolution optical images
56
what is a key feature of Confocal Laser Scanning Microscopy?
its ability to produce in-focus images of thick specimens , a process known as optical sectioning
57
Who developed the electron microscope in the 1940-50's?
Albert Claude, Keith Porter, George Palade
58
What is an electron microscope and what does it use?
a type of microscope that uses electrons to illuminate and create an image of a specimen- uses electrostatic and electromagnetic lenses to control the illumination and imaging of the specimen
59
Transmission Electron microscopy
passes a beam of electrons through a specimen to form an image on a fluorescent screen
60
What does scanning electron microscopy provide
used to provide a 3D image of cells
61
What does differential centrifugation do?
separates and isolates eukaryotic cell organelles on the basis of their size and density for use in biochemical studies
62
What is density-gradient centrifugation?
separates and purifies organelle preparations by using sedimentation through a gradient of a dense substance (sucrose)
63
What do in vitro cell culture systems enable?
study cell growth and differentiation, as well as to perform genetic manipulations required to understand gene structure and function
64
What are primary cultures?
first cell cultures established from tissues
65
How are secondary cultures form?
the cells grow until they cover the culture dish surface- removed and replated
66
Permanent (or immortal) cell lines are
embryonic stem cells (and cells derived from tumors) that frequently proliferate and indefinitely in culture
67
What percent of water do molecules account for?
70%
68
Inorganic molecules (Na+, K+, Mg+, Ca++, Cl-, HPO4-,HCO3-) constitute what % of cell mass?
1% but play critical roles in cell function
69
What do organic molecules include?
carbohydrates, lipids, proteins, and nucleic acids
70
What % do macromolecules constitute of the dry weight of most cells?
80-90% (include proteins, nucleic acids, and most carbohydates)
71
What do carbohydrates include and what does the breakdown provide?
simple sugars & polysaccharides, provide both a source of cellular energy and the starting material for the synthesis of other cell constituents
72
What are the representative simple sugars?
Monosaccharides (CH2O)n
73
How do glycosidic bonds form?
links a small number of monosaccharides together to form an oligosaccharide
74
What is the structure of polysaccharides?
hundreds/thousands of monosaccharides linked together
75
What are common polysaccharides?
glycogen and starch
76
What do lipids provide?
energy storage, major components of cell membranes, and play an important role in cell signaling
77
What are fatty acids?
the simplest lipids and consist of long hydrocarbon chains
78
What do triacylglycerols consist of?
three fatty acids linked to glycerol molecule- can be broken down for use in energy-yielding reactions
79
Phospholipids are the principal compartment of what and consist of?
cell membranes and consist of two fatty acids joined to a polar head group
80
What does a glycerol phospholipid consist of?
two fatty acids and one phosphate group, which in turn frequently attached to another small polar molecule
81
What is sphingomyelin?
the only nonglycerol phospholipid in cell membrane, contains two hydrocarbon chains that are linked to a polar head group formed from serine rather then glycerol
82
What do cell membranes contain in addition to phospholipids?
glycolipids and cholesterol
83
What does cholesterol consist of?
four hydrocarbon rings which are strongly hydrophobic, and OH group which is weakly hydrophilic
84
What are steroid hormones?
estrogen and testosterone- derivatives of cholesterol and act as signaling molecules both within and between cells
85
DNA
one of the principal informational molecules of the cell and is located in the nucleus of eukaryotic cells
86
What does mRNA carry?
carries information from DNA to the ribosomes
87
What is rRNA and tRNA involved in?
involved in protein synthesis
88
DNA and RNA are polymers of...
nucleotides, which consist of purine and pyrimidine bases linked to phosphorylated sugars
89
DNA consists of ..
two purines- adenine, guanine, and two pyrimidines- cytosine and thymine
90
RNA consists of..
adenine, guanine, thymine, and uracil
91
2-deoxyribose (sugar) links..
bases in DNA to form nucleosides
92
Ribose sugar links..
bases in RNA to form nucleosides
93
Nucleotides contain..
one or more phosphate groups
94
What do phosphodiester bonds form?
the 5' phosphate of one nucleotide and the 3' hydroxyl of another
95
How are polynucleotides synthesized?
in the 5' to 3' directions, with a free nucleotide being added to the 3' OH group of a growing chain
96
DNA is a double stranded molecule consisting of ...
two polynucleotide chains running in opposite directions- the bases inside of the molecules are joined by hydrogen bonds between complimentary base pairs
97
What do proteins execute?
the tasks directed by the genetic information of the cell
98
What is the most fundamental property of proteins?
their ability to act as enzymes, which catalyze nearly all the chemical reactions in biological systems
99
What forms proteins?
polymers of 20 different amino acids
100
What are the 4 groups of amino acids?
nonpolar, basic, acidic, polar
101
Non polar amino acids
Glycine, Alanine, valine, leucine, isoleucine, proline, cysteine, methionine, phenylalanine, tryptophan
102
Polar amino acids
serine, threonine, tyrosine, asparagine, glutamine
103
Basic amino acids
lysine, arginine, histidine
104
Acidic amino acids
aspartic acid, glutamic acid
105
What do peptide bonds join?
amino acids together
106
Fredrick Sanger was first to determine what is 1953?
the complete amino acid sequence of the hormone insulin
107
Why types of chains join insulin together?
two polypeptide chains joined by disulfide bonds
108
Christian Anfisen first demonstrated what?
that the shapes of proteins are determined by their amino acid sequence (3D conformation is critical for protein function)
109
What is x-ray crystallography?
a high resolution technique that can determine the arrangement of individual atoms within a molecule
110
How does x-ray crystallography work?
a beam of x-ray is directed at crystals of the protein- the structure of the molecule can be deduced from the pattern of scattered x rays detected on x ray film
111
John Kendrew was the first to determine what in 1958?
the 3D structure of a protein, myoglobin
112
What is the primary structure of proteins?
the sequence of amino acids in the proteins polypeptide chain
113
What is the secondary structure of proteins?
the regular arrangement of amino acids within localized regions of the polypeptide
114
What are two types of secondary structures?
a helix and b sheet
115
What is the tertiary structure of proteins?
the 3rd level and consists of the folding of the polypeptide chain as a result of interactions between the side chains of amino acids that lie in different regions of the primary sequence
116
What is the quaternary structure of proteins?
the 4th level and consists of the interactions between different polypeptide chains in proteins composed of more than one polypeptide
117
Isoelectric points have a net charge of
0
118
Why is pL of basic proteins above 7?
NH2 group is basic and at neutral pH accepts proton and become NH3+
119
Why is pL of acidic proteins below 7?
COOH group is acidic and at neutral pH donates proton and becomes COO-
120
What is the first step in order to characterize a protein?
purify the protein by separating it from other components in complex biological mixtures
121
What are the sources of proteins?
blood, tissues, cell culture, bacteria, yeast
122
Cells are disrupted by...
grinding or homogenization
123
'Crude extract' containing organelles are fractionated by..
high-speed centrifugation or ultracentrifugation
124
What are protein separations based on?
size, charge, solubility, specific biological interaction
125
Solubility: (salting out)
proteins are less stable at high salt concentrations
126
What happens when the salt concentration is increased?
as a result of the increased demand for solvent molecules, the
protein-protein interactions become stronger; the protein molecules coagulate by forming hydrophobic
interactions with each other
127
Salt can be removed using ....
dialysis
128
What is dialysis?
used to remove small molecules, such as salts from proteins
129
What is the process of dialysis?
The protein-salt solution is added to a
semipermeable membrane tube
The tube is immersed in a dilute buffer
solution
small molecules will pass through
large protein molecules will be retained in the tube
130
What is the process of gel filtration chromatography?
based on size - Molecules move through a bed of porous
beads, diffusing into the beads to greater or lesser degrees.
Smaller molecules diffuse into the pores of the beads and therefore move through the bed more slowly
larger molecules enter less or not at all and thus move through the bed more quickly.
131
Charge: Ion-Exchange chromatography
The beads are attached to ionic (charged) functional groups that interact with analyte ions of opposite charge.
Cation exchange chromatography retains cations because the stationary phase displays a negatively charged functional group
Anion exchange chromatography retains anions using positively charged functional group
132
Specific Biologic interaction: Affinity chromatography
Affinity chromatography is a specific method for purification of proteins, based on a highly specific biologic interaction such as
between antigen and antibody
enzyme and substrate
receptor and ligand.
A column matrix is derivatized with a ligand that binds to a specific protein in a complex mixture. The other proteins wash through the column.
133
High-performance liquid chromatography
is a powerful chromatographic technique for high-resolution separation of proteins, peptides, and amino acids. Separation can based on different protein characteristics
134
What is the process of HPLC?
sample is forced at high pressure in stream of mobile phase through a column of the stationary phase, sample is retarded by specific chemical or physical interactions with the stationary phase- The time at which a specific analyte elutes (comes out of the end of
the column) is a unique identifying characteristic of a given analyte
The eluates are monitored by ultraviolet absorption, refractive index, or fluorescence.
135
What does HPLC give?
high-resolution separation with high specificity and high sensitivity and is the most common technique for purification of proteins and peptides
136
What is SDS-PAGE used to separate?
is used to separate proteins
in electric field on the basis of their molecular weights.
137
What does Polyacrylamide gel -cross-linked polymer form?
a net structure though which protein molecules travel. (the smaller molecules to be separated, the higher
percentage of polyacrylamide is used)
138
The solution of proteins to be analyzed is first mixed with SDS, an anionic detergent which:
1) denatures secondary and non–disulfide–linked tertiary
structures,
2) applies a negative charge to each protein in proportion
to its mass, so that they may be separated strictly by length
(or number of amino acids).
139
What is the reducing agent used to reduce disulfide bonds?
β-mercaptoethanol
140
Charge: Isoelectric Focusing
Separation of proteins on the basis of their pI by conducting electrophoresis in gel containing a pH gradient.
141
Upon application (in IEF) a protein will move towards...
the anode or cathode until it encounters that part of the system that corresponds to its pl, where the protein has no charge and will cease to migrate
142
2D Gel electrophoresis (IEF & SDS-PAGE) what is a proteome and what is proteomics?
proteome- defined as the full compartment of proteins produced by a particular genome
proteomics- defined as the qualitative and quantitative comparison of proteomes under different conditions with the goal of further unraveling biological processes
143
How do you analyze a proteome of a cell?
proteins from a cell
are extracted and subjected to 2 dimensional gel electrophoresis (IEF in one direction followed by
SDS-PAGE in another direction).
Gel spots identified on a 2D Gel are usually attributable to one protein. If the identity of the protein is desired, the gel spot can be excised, and digested proteolytically in order to analyze
144
How to determine a protein's amino acid composition once purified?
a protein is subjected to hydrolysis, commonly in 6 mol/L HCl at 110°C in a sealed and evacuated tube for 24-48 h.
145
What happens after hydrolysis?
the free amino acids are separated on an automated amino acid analyzer using an ion-exchange column, or
by reversed-phase (HPLC). The amino acids are reacted with chromogenic or fluorogenic reagents and are separated by charge or hydrophobicity.
146
What is sequencing?
a stepwise process of identifying the specific amino acids at each position in the peptide chain
147
The cleaved peptides are sequenced using the..
Edman Degradation technique
148
How is a protein cleaved first?
by digestion by specific endoproteases, such as trypsin to obtain peptide fragments
149
What is the Edman degradation method?
sequentially removes one residue at a time from the amino end of a peptide. (PITC, Edman reagent) binds N-terminal amino acid and introduce instability in the N-terminal peptide bond that can be selectively hydrolyzed.
150
The sequences of overlapping peptides is used to obtain...
the primary structure of the protein
151
How can an unknown protein be identified?
mass spectrometry
152
What is the process of mass spectrometry?
The protein is first cleaved and masses and charges of proteolytic peptides are
used as input to a search of a database of predicted masses/charges that
would arise from digestion of a list of known proteins.
153
How to determine the 3D structure of proteins?
x-ray crystallography and nmR spectroscopy
154
What does x-ray crystallography involve?
the diffraction of X-rays by the electrons of the atoms constituting the molecule. Thus the location of atoms, in the crystal can be calculated to determine the structure of the protein
155
What is nmR spectroscopy used for?
structural analysis of small organic
compounds and is based upon the magnetic properties of an atom’s
nucleus.
156
What is allosteric regulation?
a process in which a regulatory molecule binds to a site on an enzyme that is distinct from the catalytic site
157
The regulation by GTP binding is a mechanism by which...
the activities of intracellular proteins are controlled
158
Ran/GTP-Ran/GDP
nuclear-cytoplasmic transport
159
Rab proteins
membrane fusion
160
Ras Proteins
activates a number of pathways which transmit signals downstream to other gene regulatory proteins
161
What is an activated or inactivated form?
RAS-GTP and RAS GDP
162
What is often deregulated in cancers and what does it lead to?
ras and ras related proteins, lead to increased invasion and metastasis and decreased apoptosis
163
What do protein kinases catalyze?
protein phosphorylation by transferring phosphate groups from ATP to the hydroxyl groups of the side chains of serine, threonine, or tyrosine residues
164
What do protein-serine/threonine kinases phosphorylate?
serine and threonine residues
165
What do protein-tyrosine kinases phosphorylate?
tyrosine residues
166
What do protein phosphatase reverse?
protein phosphorylation and catalyze the hydrolysis of phosphorylated amino acid residues
167
Many kinases consist of multiple subunits, each of which is an...
independent polypeptide chain
168
Many kinases are dependent on what and consist of?
cAMP-dependent protein kinase and consist of two regulatory subunits and two catalytic subunits
169
What does binding of cAMP to regulatory subunits induce?
a conformational change that leads to their dissociation from regulatory subunits
170
The free catalytical subunits are...
enzymatically active
171
Proteins can be modified by...
methylation and acetylation
172
Why are post-transitional modifications of histones are of special interest?
may regulate transcriptional activity of cells and regulate the level of different proteins in the cells
173
What do specific histone modifications result in?
more open (transcriptionally active) or condense (repressed) chromatin state
174
What happens when chromatin is open?
transcription factors can access DNA and initiate gene transcription
175
Where does histone phosphorylation occur?
serine residues and also correlates with transcriptional activation
176
Where does histone acetylation occur?
lysine residues and correlates with transcription activation
177
Where does methylation occur?
lysine and arginine residues and correlates with transcriptional repression
178
Specific histone modifications are recognized by what?
transcriptional factors or other proteins that regulate modification of chromatin and initiation of transcription-histone code
179
What is the histone code?
is a hypothesis that the transcription of genetic information encoded in DNA is in part regulated by chemical modifications to histone proteins
180
Activity of genes can also be regulated by ...
methylation of Cytosine residue on DNA molecule which would
usually inhibit the transcription
181
What is epigenetics?
is the study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence (for example DNA methylation and histone
modification).
182
What does evidence supporting epigenetics show?
these mechanisms can enable the
effects of parents' experiences to be passed down to subsequent generations
183
What is nitrosylation?
the addition of NO groups to the side chains of cysteine residues
184
The levels of proteins within cells are determined by...
rates of synthesis & rates of degradation
185
What happens with faulty or damaged proteins?
they are recognized and rapidly degraded within cells, thereby eliminating the consequences of mistakes made during protein synthesis
186
Ubiquitin is a marker that targets...
cytosolic and nuclear proteins for rapid proteolysis and recruit them to proteosome
187
What are proteasomes?
large multi-subunit protease complexes that recognize and degrade polyubiquinated proteins
188
Activation of ubiquitin and its conjugation to target protein through the series of enzymes. What are the proteins?
Activating protein, conjugating protein, ligating protein
189
What is monoubiquitination?
is not a marker for degradation but is away to modify a protein properties (regulation of transcription factor activities)
190
What is SUMO?
(small ubiquitin-related modifiers) were discovered based on their homology to ubiquitin
191
What does SUMO implicate?
don't target proteins to degradation but are implicated in variety of cellular events including regulation of transcription
192
Modifications of proteins with...
SUMO-sumoylaylation
193
Ubiquitination and sumolaytion of histones may also constitute an element of the...
histone code
194
What does the structure of a cell membrane functions to?
separate the interior of the cell from its environment and to define the internal compartments of eukaryotic cells, including the nucleus and cytoplasmic organelles
195
What do all cell membranes share?
a common structural organization: bilayers of phospholipids with associated proteins
196
What are the fundamental building blocks of all cell membranes?
phospholipids
197
What do phospholipid bilayers form?
a stable barrier between two aqueous compartments and represent the basic structure of all biological membranes
198
What do lipid bilayers behave as?
2D fluids in which individual molecules are free to rotate and move in lateral directions
199
What is cholesterols distinct role?
determining membrane fluidity
200
Jonathan Singer and Garth Nicolson gave what description to the cell?
"Fluid mosaic" when they observed that proteins are inserted into a lipid bilayer
201
Where are integral membrane proteins embedded?
within the lipid bilayer
202
What are transmembrane proteins?
integral membrane proteins that span the lipid bilayer
203
What are peripheral membrane proteins?
not inserted into the lipid bilayer but associated with the membrane indirectly
204
What does the selective permeability of biological membranes allow?
allows the cell to control and maintain its internal composition
205
What cannot diffuse freely across a lipid bilayer?
charged (ions) and most large polar molecules
206
What can cross the membrane?
small and uncharged molecules
207
What are channel proteins?
form open pores through the membrane, allowing free passage of any molecule of the appropriate size
208
What do carrier proteins do?
selectively bind and transport specific molecules such as glucose
209
What is passive transport?
a process where molecules are transported by either channel or carrier
proteins across membranes in the energetically favorable direction
210
What is active transport?
process where molecules are transported in an energetically unfavorable direction across a membrane if their transport is coupled to ATP hydrolysis as a source of
energy
211
What is cell metabolism?
the sum of many ongoing individual processes by which living cells process nutrient molecules and maintain a living state
212
Chemical reactions in biological systems are organized into sequences. What are the sequences called?
metabolic pathways
213
Control of pathways is achieved via the ... which do what?
enzymes which specifically catalyze each of the steps in a pathway
214
How to organize the reactions into pathways?
-allows doe individual reactions to be stimulated or inhibited by changing the concentration of key compounds or by chemical modification of the enzyme
-prevents very large chemical bond energy releases which would be damaging to cells
-permits branch points which allows pathways to be directed (under different circumstances) to different end products
215
What are inborn errors of metabolism?
mutation of a single gene results in the loss of function of the appropriate enzyme
216
What do enzymes increase?
the rate of chemical reactions without themselves being consumed or permanently altered by the reaction, and increase reaction rates without altering the chemical equilibrium between reactants and products
217
What is a substrate?
a molecule that is acted upon by an enzyme
218
What is a product?
a result of the reaction between the enzyme and the substrate
219
What is activation energy?
the energy required to reach the transition state, which constitutes a barrier to the progress of the reaction
220
What does the substrate bind to?
a specific region of the enzyme called the active site
221
What is a specific interaction?
the binding of a substrate to the active site of an enzyme
222
What is the simplest model of enzyme-substrate interaaction?
lock and key model- the substrate fits precisely into the active site
223
What is induced fit?
the process in which the configurations of both the enzyme and the substrate are modified by substrate binding
224
What are prosthetic groups?
small molecules bound to proteins in which they play critical functional roles
225
What are coenzymes?
low-molecular-weight organic molecules that participate in specific types of enzymatic reactions by working together with enzymes to enhance reactions rates
226
What is an example of a coenzyme which functions as a carrier of electrons in oxidation-reduction reactions?
NAD+
227
What are metabolic oxidation/reduction reactions catalyzed by?
a class of enzymes designated as dehydrogenases
228
What do these enzymes (dehydrogenases) use?
one of a limited number of cofactors as electron acceptors or donors to complete the reaction as the metabolic substrate is reduced or oxidized
229
What is oxidation?
loss of electrons from a molecule, accompanied by a loss of one or more hydrogen atoms from the molecule
230
What is reduction?
gain of electrons by a molecule, accompanied by the gain of one or more hydrogen atoms from the molecule
231
What is an important feature of most enzymes?
their activities are not constant but instead can be modulated
232
What is feedback inhibition?
a type of enzyme regulation in which the product of a metabolic pathway inhibits the activity of an enzyme involved in its synthesis
233
What is allosteric regulation?
the process wherein enzyme activity is controlled by the binding of small molecules to regulatory sites on the enzyme
234
What is phosphorylation a mechanism for?
regulating enzyme activity- the addition of phosphate groups either stimulates or inhibits the activities of many different enzymes
235
What are the two divisions of metabolism?
anabolism and catabolism
236
What is anabolism?
the metabolic process that binds larger molecules from smaller ones
237
What happens in anabolism?
energy is consumed to synthesize or combine simpler substances, such as amino acids or nucleotides, into more complex organic compounds such as enzymes and nucleic acids
238
What is catabolism?
the metabolic process that breaks down molecules into smaller units
239
What happens in catabolism?
Large polymeric molecules (polysaccharides, nucleic acids, and proteins) are processed into their constituent monomeric units (monosaccharides, nucleotides, and amino acids)
240
Complex molecules are broken down to ...
produce energy and reducing power
241
Why does ATP need to be regenerated?
ATP molecule is used within a minute of its formation, during strenuous exercise, the rate of utilization of ATP is even higher
242
The body utilizes energy from nutrients in the diet to produce what?
ATP through oxidation-reduction reactions
243
What is chemical energy in our food converted to?
reducing agents (NADH and FADH2)
244
What are the reducing agents used for?
to make ATP
245
What does ATP store?
chemical energy so that it is available to the body in a readily accessible form
246
3 groups of biological molecules are considered to be "fuels" for the body: Carbohydrates
glucose is the most abundant monomer in this group and animals- glucose is stored as glycogen
247
3 groups of biological molecules are considered to be "fuels" for the body: Proteins
the monomers of proteins (amino acids) are a significant fuel for carnivores, but are a less significant component of out omnivorous diet- provide an important reserve of fuel molecules but are only used to a large extent in circumstances of prolonged starvation
248
3 groups of biological molecules are considered to be "fuels" for the body: Fats
stored as triglycerides in adipose tissue and make up our major fuel store- the fatty acid components of triglycerides are readily oxidized to produce ATP
249
What happens in carbohydrate catabolism?
(breakdown of sugars)- glycolysis breaks glucose down into pyruvate- in eukaryotes, pyruvate moves into the mitochondria, is converted into acetyl-coA and enters the citric acid cycle
250
What happens in protein catabolism?
proteins are broken down by protease enzymes into their constituent amino acids- these amino acids are brought into the cells and can be a source of energy by being funneled into the citric acid cycle
251
What happens in fat catabolism?
triglycerides are hydrolyzed to break them down into fatty acids and glycerol- in the liver, glycerol can be converted into glucose by way of gluconeogenesis. in many tissues (heart tissue) fatty acids are broken down through a process known as beta oxidation which results in acetyl-CoA which can then be used in the citric acid cycle
252
What happens in stage 1 of catabolic processes?
breakdown of macromolecules occurs outside cells
253
What happens in stage 2 of catabolic processes?
glucose to pyruvate (occurs in cytosol), pyruvate is transformed into acetyl-CoA which is the common intermediate in the energy metabolism of carbohydrates, lipids, and amino acids (happens in mitochondria)
254
What happens in stage 3 of catabolic processes?
Acetyl-CoA enters the central metabolic engine of the cell (citric acid cycle) in the mitochondrial matrix- the citric acid cycle oxidizes acetyl-CoA to CO2 and reduces NAD+ to NADH & FAD to FADH2- the reduced nucleotides capture the energy from fuel oxidation and are the substrates for the final pathway (oxidative phosphorylation in the inner mitochondrion membrane which provides the energy for synthesis of ATP)
255
What has enabled scientists to dissect complex eukaryotic genomes and probe the functions of genes?
gene cloning
256
The presence of what is a general property of the genomes of complex eukaryotes?
large amounts of noncoding sequences
257
What constitutes most of the DNA of higher eukaryotes?
non-coding sequences
258
What is a gene?
a segment of DNA that is expressed to yield a functional product
259
What are spacer sequences?
long DNA sequences that lie between genes
260
What are exons?
segments of coding sequence
261
What are introns?
(intervening sequences) are segments of noncoding sequences
262
What is the entire gene transcribed to yield:?
a long RNA molecule and the introns are removed by splicing
263
What does the gene encoding the adenovirus hexon consist of?
four exons interrupted by three introns
264
What is RNA assembled from?
several distinct blocks of sequences originated from different parts of viral DNA
265
What do introns not specify and what do they play a role in?
do not specify the synthesis of a cellular product but play a role in controlling gene expression
266
When does alternative splicing occur?
when exons of a gene are joined in different combinations, resulting in the synthesis of different proteins from the same gene
267
What are the complexes between eukaryotic DNA and proteins called?
chromatin- contain about twice as much protein as DNA
268
What are histones?
small proteins containing a high proportion of the basic amino acids, arginine and lysine that facilitate binding to the negatively charged DNA molecule
269
What are the 5 major types of histons?
H1, H2A, H2B, H3, H4
270
What is the basic structural unit of chromatin and who first described it?
Nucleosome, Roger Kornbert in 1974
271
What do nucleosome core particles contain?
145 base pairs of DNA wrapped around a histone octamer consisting of two molecules each of H2A, H2B, H3, H4
272
What is bound to the DNA as it enters each nucleosome core particle?
H1
273
What is euchromatin?
decondensed transcriptionally active interphase chromatin
274
What is heterochromatin?
condensed transcriptionally inactive chromatin and contains highly repeated DNA sequences
275
What is a centromere?
a specialized region of the chromosome that plays a critical role in ensuring the correct distribution of duplicated chromosomes to daughter cells during mitosis
276
What is the kinetochore?
the protein structure in eukaryotes which assembles on the centromere and links that chromosome to microtubule polymers from the mitotic spindle during mitosis
277
What are telomeres?
the sequences at the ends of eukaryotic chromosomes
278
What do the telomere DNA sequences consist of?
repeats of a simple-sequence DNA containing clusters of G residues on one strand
279
What did traditional biologists believe?
single gene and protein experiments --> understanding individual molecules and pathways
280
What did systems biologists believe?
genome and proteome-wide experiments ---> understanding integrated cell processes
281
Large-scale screens based on RNA interference are being used to...
systematically dissect gene function in a variety of organisms
282
The normal function of RNA interference inside the cells depends on the production of...
double stranded RNA
283
How can complimentary RNA strands be produced?
by transcription of both template DNA strands of some genes
284
What processes double-stranded RNA undergoes?
double stranded RNA is processed by dicer to small inhibitory RNA
285
What is the function of siRNA?
siRNA can form a molecular complex with proteins (RISC) that strip away the sense strand of RNA, making the (iRNA) available for base pairing with mRNA
286
What is the role of iRNA?
iRNA targets a specific mRNA for destruction, resulting in the inhibition of the biological function served by the protein coded for by the mRNA
287
What must occur each time a cell divides?
its entire genome must be duplicated
288
What is the enzyme that catalyzes the synthesis of DNA?
DNA polymerase
289
What plays distinct roles in DNA replication and repair?
multiple different DNA polymerases
290
How many known DNA polymerases are there in prokaryotes?
5
291
What is the main polymerase in bacteria?
Pol III
292
How many DNA polymerases are there in eukaryotes?
15
293
What does Pol a complex contain?
primase which synthesizes an RNA primer
294
What is Pol b implicated in?
repairing DNA
295
What does Pol y replicate?
mitochondrial DNA
296
Which polymerase is the main polymerase in eukaryotes?
Pol δ
297
What is the structure of DNA?
a double helix with the bases on the inside and the sugar-phosphate backbones on the outside of the molecule
298
What are bases on opposite strands paired by? (DNA)
hydrogen bonds between adenine and thymine and between guanine and cytosine- two DNA strands run in opposite directions, defined by the 5' and 3' groups of deoxyribose
299
What initiates DNA replication?
partial unwinding of the double helix at the replication fork, facilitated by DNA helicase
300
What enzyme moves into position as the DNA strands separate?
DNA polymerase
301
In which direction do all polymerases synthesize DNA?
5' to 3' direction
302
Where can DNA polymerases add a new deoxyribonucleotide?
a preformed primer strand that is hydrogen-bound to the template
303
What is the start point for DNA polymerase?
a short segment of RNA primer, laid down complementary to the DNA template by an enzyme known as primase
304
Why can only one new DNA strand begin at the 3' end of the template DNA?
the original DNA strands are complementary and run antiparallel
305
How does the other DNA strand grow?
opposite direction, resulting in discontinuous replication
306
What are the short sections of new DNA called?
Okazaki fragments
307
Who discovered Okazaki fragments?
Japanese researcher
308
How are the Okazaki fragments joined together?
by the action of an enzyme called DNA ligase, which ligates the pieces together by forming the missing phosphodiester bonds
309
How is the replication described when each new helix contains one old template strand and one newly synthesized strand?
semi-conservative
310
What initiates the process of converting DNA information into proteins?
synthesis of mRNA molecules - known as transcription
311
How is transcription similar to DNA replication?
involves unwinding a small section of the DNA double helix and exposing the bases on the two strands
312
What is the difference between transcription and DNA replication regarding the copying of DNA strands?
transcription- only one of the two DNA strands is transcribed into mRNA
DNA replication- both strands are copied (transcribed DNA strand is called the template strand)
313
How many nuclear RNA polymerases do eukaryotes have?
3
314
What is the role of RNA polymerase I?
transcribes ribosomal RNA
315
What is the role of RNA polymerase II?
transcribes messenger RNA and most small nuclear RNA
316
What is the role of RNA polymerase III?
transcribes transfer RNA
317
How are primary mRNA'S transcripts processed in eukaryotic cells?
synthesized as larger precursor RNA's which are processed by splicing out introns and ligating exons into the mature mRNA
318
What is the promotor site?
the starting point of a gene is marked by a certain base sequence
319
What does the promotor of protein-encoding genes contain?
binding sites for the basal transcription complex and RNA polymerase II (normally within 50 bases upstream of the transcription initiation site)
320
What is found in the core promotor for RNA polymerase II?
contains a TATA box- DNA recognition sequence for the TATA box binding protein
321
What does binding of TBP to the TATA box initiate?
transcription complex assembly at the promotor
322
What additional elements do some genes have?
enhancer elements which can be thousands of bases upstream or downstream of the transcription initiation site
323
What is the role of enhancer elements?
in combination with upstream control elements, regulate and amplify the formation of the basal transcription complex
324
Where does mRNA travel after it has the DNAs intructions?
out of the nucleus to the cytoplasm where protein synthesis takes place
325
What is the next step after transcription?
translation- process of making proteins
326
What is a ribosome made of?
a small subunit and a large subunits
327
What is the role of tRNA?
transfer RNA- is responsible for bringing in the proper amino acids to the site of protein synthesis
328
What is a series of three nucleotides bases on a DNA molecule called?
a triplet
329
What is a set of three nucleotide bases on an mRNA molecule called?
a codon
330
What is a set of three nucleotide bases on a tRNA molecule called?
an anticodon
331
How is the anticodon related to mRNA codons?
the anticodon on tRNA is complementary to the mRNA codons
332
What is found at the "other end" of the tRNA molecule?
there is an "acceptor" site where the tRNA's specific amino acid will bind
333
How many types of amino acids can each type of tRNA molecule be attached to?
each type of tRNA molecule can be attached to only one type of amino acid
334
How many stages does protein synthesis occur in?
3 stages- initiation, elongation, and termination
335
What happens during the initiation stage of protein synthesis?
the small unit of the ribosome encounters an mRNA in the cytoplasm and the mRNA message is positioned between the two ribosome subunits
336
What acts as a "start" signal for the translation machinery during initiation?
the first A-U-G codon on the 5' end of the mRNA acts as a 'start' signal
337
What does the start codon (A-U-G) code for?
the introduction of a methionine amino acid
338
Is the start codon always the same in all mRNA molecules?
Yes, the start codon (A-U-G) and the methionine amino acid - it codes for will always be the first in any and all mRNA molecules
339
When is initiation complete?
when the methionine tRNA occupies one of the two binding sites on the ribosome
340
What happens during elongation in protein synthesis?
incoming tRNA binds to the A site next to where the tRNA with the methionine attached is on the P site
341
How does the correct tRNA attach during elongation?
attaches by having an anticodon that is complementary to the codon of the A site on the mRNA
342
What enzyme forms the peptide bond during elongation?
peptidyl transferase forms the peptide bond between the two amino acids
343
What happens after the peptide bond is formed?
the tRNA on the P site leaves and passes its amino acid on the tRNA on the A site
344
Where does the tRNA with the two amino acids move to after passing the amino acid?
moves to the P site, holding the growing protein
345
How does the ribosome expose a new A site during elongation?
the ribosomes slides down three bases (1 codon on the mRNA) exposing a new A site by the action of a translocase
346
What happens during termination of protein synthesis?
a 'stop' codon signals the end of the process
347
Why does protein synthesis stop at a stop codon?
there is no tRNA that is complementary to the stop codon, so protein synthesis stops
348
What role does the releasing factor play in termination?
frees the newly made polypeptide chain from the last tRNA
349
What happens to the mRNA molecule during termination?
the mRNA molecule is released from the ribosomes as the small and large subunits fall apart
350
What determines the fate of the mRNA molecule after termination?
Depending on how much of that particular protein is needed, the mRNA can either be re-translated or degraded. All mRNA messages are eventually degraded when the protein is no longer needed.
351
What does the presence of a nucleus allow?
gene expression to be regulated by post transcriptional mechanisms (such as alternative splicing) - enables genetic material to be protected (adding a layer of transcriptional control)
352
What does the nuclear envelope separate?
the contents of the nucleus from the cytoplasm and provides the structural framework of the nucleus
353
What does the nuclear envelope consist of?
complex structure- consists of two nuclear membranes (inner and outer), and underlying nuclear lamina, and nuclear pore complexes
354
How does the internal composition of the nucleus get established?
the selective traffic of proteins and RNA's through the nuclear pore complexes
355
What is the relationship between the outer nuclear membrane and the rough ER membranes?
outer nucleus membrane is continuous with the membranes of the rough ER
356
What is the critical function of the nuclear membranes?
act as a barrier that separates the contents of the nucleus from the cytoplasm
357
Where is the inner and outer nuclear membranes joined at?
nuclear pore complex
358
What does the nuclear lamina underly?
the inner nuclear membrane and is a fibrous meshwork that provides structural support to the nucleus
359
Where do lamins extend through?
in a loose meshwork throughout the interior of the nucleus
360
What are lamins?
60-80 kDa fibrous proteins that make up the nuclear lamina
361
What do lamins associate with?
each other to form higher-order structures like other intermediate filament proteins
362
What do lamins bind to?
specific inner nuclear membrane proteins such as emerin and the lamin B receptor and bind to chromatin through histones as well as other chromatin proteins
363
What are the lamins connected to?
the cytoskeleton by LINC complexes that span the inner and outer membranes
364
What is a nuclear membrane?
a phospholipid bilayer permeable only to small nonpolar molecules
365
What are nuclear pore complexes?
are the only channels through which most polar molecules, ions, and macromolecules (proteins, RNA) can travel between the nucleus and the cytoplasm
366
What are the two different mechanisms molecules can travel through the nuclear pore complex?
passive diffusion or selective transport
367
What does a nuclear pore complex consist of?
a structure with eightfold symmetry organized around a large central channel, which is the route that the proteins and mRNAs cross through
368
What does the nuclear pore complex consist of from a 3D view?
eight spokes attached to rings on the cytoplasmic and nuclear sides surrounding the central channel
369
Where are the spoke-ring complexes anchored?
at the sites of fusion between the inner and outer membrane
370
What structures form the nuclear basket-like structure on the nuclear side?
protein filaments extend from both cytoplasmic and nuclear rings
371
What regulates transport through the central channel of the nuclear pore complex?
proteins lining the central channel
372
What proteins are imported from the cytoplasm to the nucleus?
histones, DNA & RNA polymerases, transcription factors, and splicing factors
373
How are these proteins tagged for import into the nucleus?
tagged with NLS- specific amino acid sequences recognized by transport receptors that direct their transport through the nuclear pore complex
374
Who mapped the first NLS and when?
Alan Smith in 1984- with simian virus antigen which is localized to the nucleus of infected cells
375
What happens if there is a mutation in the NLS?
mutation of a single Lys residue in the NLS prevents nuclear import
376
What are the nuclear localization signals generally composed of?
short stretches of basic amino acid residues, such as lysine and arginine
377
What is the T antigen nuclear localization signal?
a single stretch of amino acids
378
What does the nuclear localization signal of nucleoplasmin consist of?
Lys-Arg sequence followed by Lys-Lys-Lys-Lys sequence ten amino acids downstream (called bipartite)
379
What are nuclear transport receptors?
proteins that recognize nuclear localization signals and mediate transport across the nuclear envelope
380
What are karyopherin proteins?
nuclear transport receptors- can be exportins or importins
381
What are importins?
transport macromolecules to the nucleus from the cytoplasm
382
What are exportins?
transport macromolecules from the nucleus to the cytoplasm
383
What proteins regulates the movement of macromolecules through the nuclear pore?
Ran regulates the movement of macromolecules through the nuclear pore
384
What type of protein in Ran?
one of several small GTP-binding proteins
385
How is the activity of Ran regulated?
by GTP binding and hydrolysis
386
What does RanGAP do?
RanGAP- Ran GTPase activating protein, exchanges Ran GTP for Ran GDP and localizes it to the cytoplasm
387
What does RanGEF do?
RanGEF, Ran guanine nucleotide exchange factors, exchanges Ran GDP for Ran GTP and localizes it to the nucleus
388
Where is there a high concentration of Ran GTP and Ran GDP?
Ran GTP- in the nucleus
Ran GDP- in the cytoplasm
389
What are NLS recognized by?
importins
390
What happens to the complex after importins recognize the NLS?
the complex is translocated through the nuclear pore complex
391
What occurs when Ran?GTP binds to importin in the nucleus?
binding of Ran/GTP to importin in the nucleus changes importin conformation
392
What happens after the conformation of importin changes?
the cargo (protein) is released
393
What occurs to the importin/Ran/GTP complex after cargo release?
the importin/Ran/GTP complex is re-exported through the NPC, where Ran GAP hydrolyzes the GTP to GDP
394
What are nuclear export signals?
specific amino acid sequences that target proteins for export from the nucleus
395
What happens to cargo proteins in the nucleus in association with Ran/GTP?
in the nucleus, exportins form a stable complex with cargo proteins in association with Ran/GTP
396
Where does the complex with cargo proteins go through?
the complex is translocated to the cytoplasmic side through the nuclear pore complex where Ran GTP hydrolyzes the GTP to GDP
397
What occurs after the GTP is hydrolyzed?
release of Ran/GDP followed by dissociation of the cargo
398
What happens to exportin after cargo release?
exportin is then translocated back to the nucleus
399
What are the two ways transcription factor import into the nucleus are managed?
transcription factors associate with cytoplasmic proteins that mask their nuclear localization signals- transcription factors are maintained in the cytoplasm by phosphorylation at the NLS
400
Rather than randomly winding around one another, each chromosome occupies what?
a discrete region of the nucleus
401
What does the nuclei of mammalian cells contain?
clustered sites of DNA replication within which the replication of multiple DNA molecules takes place
402
Components of the mRNA splicing machinery are concentrated in what?
discrete nuclear bodies termed nuclear speckles
403
What does the Nuclei contain?
several other types of distinct structures, such as PML bodies-sites of accumulation of different transcription factors
404
What does each nucleolar organizing region contain?
a cluster of tandemly repeated rRNA genes separated from each other by non-transcribed spacer DNA
405
What is the primary transcript of the rRNA genes?
large 45S pre-rRNA, which contains the 18S, 5.8S, and 28S rRNAs
406
What does the formation of ribosomes involve?
the assembly of the ribosomal precursor RNA with both ribosomal proteins and 5S rRNA
407
When does the association of ribosomal rRNA begin?
while the pre-rRNA is still being synthesized
408
What combines with ribosomal proteins in the nucleolus to form pre-40S and pre-60S ribosomal subunits?
rRNA molecules and the 5S rRNA combine with the ribosomal proteins in the nucleolus to form pre 40S and pre 60S ribosomal subunits
409
What is in oocytes?
the rRNA genes are amplified to support the synthesis of the large numbers of ribosomes required for early embryonic development
410
What are the three distinguishable regions of the nucleoli?
fibrillar center, dender fibrillar component, and a granular component
411
What do these regions (regions of the nucleoli) thought to represent?
are thought to represent the sites of progressive stages of rRNA transcription, processing, and ribosome assembly
412
How are eukaryotic cells distinguished from prokaryotic cells?
by the presence of membrane-enclosed organelles within their cytoplasm
413
What is the endoplasmic reticulum?
a network of membrane-enclosed tubules and sacs that extends from the nuclear membrane throughout the cytoplasm
414
What is the rough ER covered by?
ribosomes on its outer surface and is involved in protein metabolism
415
What is the transitional ER involved in?
protein processing and is where vesicles exit to the golgi apparatus
416
What is the smooth ER involved in?
lipid metabolism and is not associated with ribosomes
417
What is the secretory pathway?
a cellular process where proteins are synthesized, processed, and transported to their final destination outside the cell
418
What happens during the chase phase in the secretory pathway?
cells are incubated in media containing nonradioactive amino acids, allowing labeled proteins to be detected in the golgi
419
Where do proteins travel after the golgi during a longer chase?
proteins travel from the golgi to the cell surface in secretory vesicles, which then fuse with the plasma membrane to release their contents outside of the cells
420
What happens after a short pulse of radioactive amino acids in the secretory pathway?
newly synthesized proteins are localized to the rough ER
421
What is the pathway for proteins in the secretory pathway?
rough ER ---> Golgi ---> secretory vesicles ---> cell exterior
422
How are proteins destined to remain in the cytosol or other organelles synthesized?
proteins destined to remain in the cytosol or to be incorporated into the nucleus, mitochondria, chloroplasts, or peroxisomes are synthesized on free ribosomes and released into the cytosol
423
What does the entrance of proteins into the ER represent?
a major branch point for the traffic of proteins within eukaryotic cells
424
Where are most proteins translocated in mammals?
into ER while their translation is still in progress
425
What are proteins targeted to?
to the ER based on localization sequences that eventually get cleaved
426
What is the first step in targeting proteins to the ER?
the association of ribosomes with ER
427
David Sabatini and Gunter Blobel first proposed what in 1971?
that the signal for ribosome attachment to the ER might be an amino acid sequence near the amino terminus of the growing polypeptide chain
428
What are microsomes?
small vesicles formed from the endoplasmic reticulum when cells are disrupted, so can be used in experiments instead of ER
429
What happened when the secretory protein mRNA was translated on free ribosomes?
the proteins produced were slightly larger than the normally secreted protein
430
What occurred when microsomes were added during translation?
the growing polypeptide chains were incorporated into the microsomes
431
How were the signal sequences removed?
by proteolytic cleavage
432
What does an amino terminal leader sequence target?
the polypeptide chain to the microsomes and is then cleaved by a microsomal protease
433
What is the mechanism by which secretory proteins are targeted to the ER during translation?
the mechanism involves signal sequences that span about 20 amino acids, including a stretch of hydrophobic residues
434
What happens as proteins emerge from the ribosome?
signal sequences are recognized and bound by signal recognition particles
435
SRP consisted of SRP proteins are associated with what?
small cytoplasmic RNA
436
What are SRP receptors?
are proteins on the membrane of the ER that bind the signal recognition particle
437
What is a translocon?
is a membrane proteinous channel through which polypeptide chains are transported into the ER
438
What do signal peptidase cleave?
the signal sequence and releases it into the lumen of the ER
439
What happens to proteins destined for secretion from the cell or residence within the lumen of certain organelles?
these proteins are translocated across the ER membrane and released into the lumen of the ER
440
Where are integral membrane proteins embedded?
in the ER membrane by hydrophobic sequences that span the phospholipid bilayer
441
How is the lumen of the ER related to the exterior of the cell?
is topologically equivalent to the exterior of the cell
442
What does this topological equivalence imply for plasma membrane proteins?
implies the domains of plasma membrane proteins that are exposed on the cell surface corresponds to the regions of polypeptide chains that are translocated into the ER lumen
443
How are most transmembrane proteins destined for other compartments in the secretory pathway delivered?
in transport vesicles
444
What is preserved regarding the orientation of these proteins during delivery?
the orientation of the proteins is preserved
445
What needs to happen for polypeptides to be useful?
polypeptides must fold into distinct 3D conformations- in many cases, multiple polypeptide chains must be assembled into a functional complex
446
Where do many protein folding and processing events occur for proteins in the secretory pathway?
occur either during translocation across the ER membrane or within the ER lumin
447
What processes occur in the rough ER?
protein folding, assembly of multisubunit proteins, disulfide bond formation, the initial stage of glycosylation, and the addition of glycolipid anchors to some plasma membrane proteins occur
448
What is glycosylation?
a process in which many proteins, particularly in eukaryotic cells, are modified by the addition of carbohydrates
449
What are glycoproteins classified as?
either N-linked (on asparagine) or O-linked (on serine or threonine) depending on the site of attachment of the carbohydrate side chain
450
What are most glycoproteins in eukaryotic cells destined for?
secretion or incorporation to plasma membrane which are transferred into ER where N-linked glycosilation is initiated
451
What is the first step of N-glycosylation?
the transfer of a common oligosaccharide consisting of 14 sugar residues to an asparagine residue within the sequence (Asn-X-Ser or Asn-X-Thr) of a growing amino chain
452
Where is the oligosaccharide assembled before being transferred in N-glycosylation?
within the ER on a lipid carrier called dolichol
453
What happens after the oligosaccharide is transferred in N-glycosylation?
after transfer, 3 glucose residues are removed, with more modification occurring in the golgi
454
How does O-linked glycosylation differ from N-glycosylation?
O-linked- sugars are added one residue at a time usually in the Golgi
N-linked- a oligosachride consisting of 14 sugar residues is added to asparagine residue in ER, removal of some residues in ER, removal of some residues and addition of other sugars in Golgi
455
How are some proteins attached to the plasma membrane?
by glycolipids, specifically glycosylphosphatidylinositol (GPI) anchors
456
Where are GPI anchors made?
in the ER membrane
457
When are GPI anchors added to the protein?
to the c-terminus of the protein in the ER immediately after the completion of protein synthesis
458
How are proteins attached to glycolipids transported to the cell surface?
like transmembrane proteins, proteins attached to glycolipids are transported to the cell surface via the secretory pathway
459
How are proteins oriented in the plasma membrane when attached to glycolipids?
oriented in the plasma membrane with the protein exposed outside of the cells (inside the ER lumen equals outside of the cell)
460
Why are many proteins synthesized in the ER rapidly degraded?
because protein folding in the ER is not efficient, leading to misfolded proteins
461
What happens to misfolded proteins in the ER?
misfolded proteins are recognized and sent back out to the cytosol to be degraded by the proteasome through a pathway called ER-associated degradation
462
What occurs to properly folded proteins in the ER?
exit the ER to the Golgi and beyond, continuing along the secretory pathway
463
What is the unfolded protein response?
a cellular stress response in which an excess of unfolded proteins in the ER leads to general inhibition of protein synthesis, increased expression of chaperones, and increased proteasome activity
464
Where are membrane lipids primarily synthesized?
in the ER
465
Why are membrane lipids synthesized in association with existing cellular membranes?
Membrane lipids are synthesized in association with existing cellular membranes because they are extremely hydrophobic and cannot be synthesized in the aqueous environment of the cytosol.
466
How are phospholipids synthesized on the cytosolic side of the ER membrane?
Phospholipids are synthesized on the cytosolic side of the ER membrane, allowing the hydrophobic fatty acid chains to remain buried in the membrane while membrane-bound enzymes catalyze their reactions with water-soluble precursors in the cytosol
467
What are glycerol phospholipids synthesized from in the ER membrane?
Glycerol phospholipids are synthesized in the ER membrane from two fatty acids (linked to coenzyme A) and glycerol-3-phosphate, yielding phosphatidic acid, which is then inserted into the membrane. Phosphatidic acid is converted to diacylglycerol (DAG), and different polar headgroups are attached to DAG to yield different phospholipids.
468
What are the three main types of lipids composing the membranes of eukaryotic cells?
phospholipids, glycolipids, and cholesterol.
469
Why are the phospholipids added only to the cytosolic half of the ER membrane?
so they are added only to the cytosolic half of the bilayer
470
How are phospholipids translocated across the ER membrane to ensure even growth of both halves of the bilayer?
by flippases, membrane proteins that catalyze the rapid translocation of phospholipids, resulting in even growth of both halves of the bilayer
471
What are the two other membrane lipids synthesized in the endoplasmic reticulum (ER)?
Cholesterol and ceramide are synthesized in the ER.
472
What is the role of the Smooth ER besides lipid synthesis?
The Smooth ER is involved in the production of steroid hormones and detoxification of organic chemicals.
473
Where is Smooth ER abundant, and why?
Smooth ER is abundant in cell types that are particularly active in lipid metabolism because it plays a large role in lipid metabolism and detoxification.
474
What is one of the main functions of smooth ER in liver cells?
One of the main functions of smooth ER in liver cells is detoxification.
475
How does smooth ER adapt to detoxification needs?
Smooth ER can double its surface area within a few days to assist with detoxification, returning to its normal size when the assault has subsided.
