Term
| The ___ is a network of filamentous structures,which consists of what three things? These together form an elaborate interactive network. |
|
Definition
Cytoskeleton
microtubules, microfilaments(actin filaments) and intermediate filaments. |
|
|
Term
| The cytoskeleton is made up of polymers of ___ held together by weak, ___ which can disassemble rapidly. |
|
Definition
protein subunits
noncovalent bonds |
|
|
Term
| What are the 5 roles of the cytoskeleton? |
|
Definition
–Serves as a scaffold providing structural support and maintaining cell shape.
–Serves as an internal framework to organize organelles within the cell.
–Directs cellular locomotion and the movement of materials within the cell.
–Facilitates cell mobility (crawling, swimming).
–Involved in many activities associated with cell division. |
|
|
Term
| ___ are hollow, cylinderical structures, which are 25nm in diameter and 4nm thick for their wall. |
|
Definition
|
|
Term
| The microtubule is a set of globular proteins arranged in longitudinal rows called __. How many do they contain? How are each of these assembled? |
|
Definition
protofilaments
13
Each protofilament is assembled from dimers of α- and ß-tubulin subunits assembled into tubules with plus (ß) and minus (α) ends. |
|
|
Term
| All of the protofilaments of a microtubule have the same polarity. Consequently the entire polymer has polarity. One end of a microtubule is known as the plus end and is termiated by a row of ___ the opposite end is the minus end and is terminated by a row of _____. As discussed later in the chapter the structural polarity of microtubules is an important factor in ___ |
|
Definition
beta tubulin subunits
alpha tubulin subunits
the growth of these structures and their ability to participlate in directed mechanical activities. |
|
|
Term
| Microtubules prepared from living tissue typically contain additional proteins called ___ which are comprised of what? |
|
Definition
microtubule associated proteins (MAP)
-comprised of a heterogeneous collection of proteins. |
|
|
Term
| What are the functions of MAPs? How are they regulated? What can they connect? |
|
Definition
–MAPs attach to the surface of microtubules to increase their stability and promote their assembly.
–MAPs are regulated by phosphorylation of specific amino acid residues.
–MAPs can connect microtubules to other structures or other microtubules. |
|
|
Term
| Microtubules are stiff enough to resist forces that might compress or bend the fiber. WHat does this property allow? |
|
Definition
| determines the shape of the cell and provides mechanical support |
|
|
Term
| Microtubules maintain the __ of cells. Treatement of cell swith microtubule disrupting drugs can seriously affect the location of membranous organelles including the ER and Golgi complex. |
|
Definition
|
|
Term
| How do microtubules play a role in plant cells? |
|
Definition
| microtubules help maintain cell shape by influencing formation of the cell wall. Cellulose is laid down parallel to microtubules. Elongation is commonly restricted to one axis. |
|
|
Term
| Microtubules facilitate movement of vesicles between compartments. How is this known? |
|
Definition
| because specific disruption of these cytoskeletal elements brings the movements to a halt. |
|
|
Term
| What is axonal transport do?The axon of an individual motor neuron consists of a malfunctioning center called the ___. What is it? |
|
Definition
Movement of neurotransmitters and other materials across the cell.
Movement away from the cell body (anterograde) and toward the cell body (retrograde).
Mediate tracks for a variety of motor proteins.
cell body. a rounded portion of the cell that resides within the spinal cord. |
|
|
Term
–Molecular motors convert ___ from ATP into ___
–Molecular motors move ___ along their cytoskeletal track in a stepwise manner. |
|
Definition
chemical energy; mechanical energy.
unidirectionally |
|
|
Term
Collectively, motor proteins can be grouped into 3 broad superfamilies, what are they?
What is the difference between them?
Why dont motor proteins use intermediate filament tracks?
|
|
Definition
kinesins, dyneins, and myosins.
kinesins and dyneins move along microtubules, whereas myosins move along microfilaments.
Because intermediate filaments are not polarized and thus could not provide directional cues to the motor. |
|
|
Term
What is kinesin 1? What is kinesin?
Each kinesin includes a pair of __, connected to a rod like stalk. |
|
Definition
member of a superfamily called KLP's (kinesin-
like proteins)
A tetremer of 2 identical heavy chains and two identical light chains
glubular heads (motor domain, hydrolyzing ATP) |
|
|
Term
| What kind of motors are kinesins? |
|
Definition
| plus end directed microtubular motors (exception is kinesin-14 whichi s minus end directed and kinesin 13 does not move and acts in microtubule dynamics) |
|
|
Term
–Kinesins move along a single protofilament of a microtubule at a velocity proportional to ___
___ nm moved (the length of a dimer) per ATP used.
–Movement is ____: motor protein moves along an
individual microtubule for a long distance without
falling off. |
|
Definition
to the ATP concentration.
8
processive |
|
|
Term
| In most cells, KLPs move cargo toward the cell's ___. This determines cargo specificity. |
|
Definition
|
|
Term
__ is responsible for the movement of cilia and flagella
___ is a huge protein with a globular force generating head. It is a multimer with 2 identical heavy chains and a variety of intermediate and light chains |
|
Definition
dynein
Cytoplasmic dynein |
|
|
Term
| What kind of motor is a cytoplasmic dynein? What does it require? |
|
Definition
minus end directed microtubular motor
requires an adaptor (dynactin) to interact with membrane bounded cargo |
|
|
Term
What are MTOCs?
What is the major MOTC in animal cells? |
|
Definition
–specialized structures for the nucleation (the initial organizing structure) of microtubules that precedes initiation and elongation of microtubules.
Centrosome
|
|
|
Term
| What is a centrosome? It has a pinwheel arrangement |
|
Definition
•It contains (usually) twobarrel-shaped centrioles at right angles and is surrounded by pericentriolar material (PCM), which is the terminus of the minus end of microtubules.
•The plus (growing) end is away from the centrosome.
•The proportion of microtubules that remain connected to the centrosome varies among different cell types. |
|
|
Term
| The polarity of microtubules is always the same: the __is associated with the centrosome and the ___ or growing end is situated at the opposite tip |
|
Definition
|
|
Term
| What is a structure where outer microtubules in a cilia and flagella are generated. They are identical in structure to centriole |
|
Definition
|
|
Term
| Do plant cells have MTOCs? |
|
Definition
| No, plant cells lack MTOCs and their microtubules are organized around the surface of the nucleus and widely throughout the cell cortex (the cytoplasmic region immediately inside the plasma membrane). |
|
|
Term
All MTOCs play similar roles in all cells. What are they?
What is g-tubulin? |
|
Definition
–control the number of microtubules, their polarity, the number of protofilaments per microtubule, and the time and location of their assembly.
–found in all MTOCs and in microtubule initiation sites in plants, and is critical for microtubule nucleation. |
|
|
Term
| Microtubules are highly variable in their stability. How so? |
|
Definition
–Cytoskeleton and mitotic spindle (involved in cell division) are highly labile (subject to disassembly).
–Neuronal microtubules are more stable.
–Cilia and flagella microtubules are highly stable.
–Disruption of non-covalent bonds- MAPs and Taxol stabilize MTs, other chemicals disrupt MTs. |
|
|
Term
| What are the 4 distinct arrays of microtubules in a dividing plant cell? |
|
Definition
–Widely distributed throughout the cortex.
–Making a single transverse band (preprophase band) that
predicts the site of cell division.
–In the form of a mitotic spindle.
–As a phragmoplast assisting in the formation of the cell
wall of daughter cells. |
|
|
Term
| The changes in spatial organization of microtubules are a combination of 2 mechanisms. What are they? |
|
Definition
•Rearrangement of existing microtubules (in growing cells)
•Disassembly of existing microtubules and reassembly of new ones in different locations. (phragmoplast -> cortical array -> preprophase band). |
|
|
Term
–In plants, newly formed microtubules branch at an angle of ___ |
|
Definition
| pre-existing microtubules. g-tubulin-mediated initiation. |
|
|
Term
Insight into factors that influence microtubule assembly and disassembly came from ___
Lack of MTOC/g-tubulin template can lead to variations in ___
Microtubules grow by addition of __
What is required for microtubule assembly?
|
|
Definition
studies in vitro
microtubule diameter.
alpha-beta dimers
GTP
|
|
|
Term
| GTP on the beta subunit is hydrolyzed to GDP once the dimer is ___ After disassembly, replacement of bound GDP by new GTP on the beta subunit ___ the tubulin dimer. |
|
Definition
bound (GTP on alpha subunit is not hydrolyzed and not exchanged).
recharges |
|
|
Term
| In the structural cap model of dynamic instability, cap closure is accompanied by___. ___ are not favored structurally and cause strain. They must be stabilized by MAPs or other factors. What does strain facilitate? |
|
Definition
hydrolysis of GTP on beta subunit
Linear arrangement of GDP bound dimers
rapid disassembly |
|
|
Term
| What are the 2 tenants for Dynamic instability? |
|
Definition
–) Growing and shrinking microtubules can coexist in the same region of a cell.
–2) A given microtubule can switch back and forth between growing and shortening phases in an unpredictable (stochastic) manner. |
|
|
Term
| Dynamic instability is an inherent property of the ___ of the microtubule |
|
Definition
|
|
Term
| Proteins called ___ regulate the rate of growth and shrinkage (as well as attachment points) |
|
Definition
|
|
Term
| A series of photographs show the changes in length of a single microtubule in the growth cone of a neuron. How was this done? |
|
Definition
| fluorescently labeled tubulin at low concentration to product green fluorescent speckles along the length of microtubules. |
|
|
Term
| ___ and ___ are hairlike motile organelles that project from the surface of a variety of eukaryotic cells. Bacteria also possess structures referred to as ___ but prokaryotic flagella are simple filaments that bear no evolutionary relationship to their eukaryotic counterparts. They are composed of __ |
|
Definition
| Cilia and flagella ; flagella ; flagellin |
|
|
Term
| Cilia and flagella have the same structures but different ? |
|
Definition
|
|
Term
| Cilia can be likened to an oar as it moves the cell in a direction perpendicular to the cilium itself. The cilium is maintained in a rigid state as it pushes against the surrounding medium. They tend to occur in __ numbers on a cells surface and their beating activity is usually coordinated. What are they used for? |
|
Definition
| Large ; Can be used for motility(microorganisms) or to move fluid (like mucus in lungs) |
|
|
Term
| Explain the process of a ciliary beat |
|
Definition
| In its power stroke the cilium is maintained in a rigid state as it pushes against the surrounding medium. in its recovery stroke the cilium becomes flexible offering little resistance to the medium. |
|
|
Term
| flagella exhibit a variety of different beating patterns (waveforms), depending on the cell type. The single-celled alga pictured pulls itself forward by waving its 2 flagella in an ___ manner that resembles the breast stroke of a human swimmer. |
|
Definition
|
|
Term
| The structure of cilia and flagella –contains a central core (___) consisting of microtubules in a 9 + 2 arrangement (9 peripheral doublets surrounding a central pair of microtubules). |
|
Definition
|
|
Term
| ____ contain a complete A tubule and an incomplete B tubule (10-11 filaments instead of 13) |
|
Definition
| Peripheral (outer) doublets |
|
|
Term
| The basic structure of the axoneme includes ___ |
|
Definition
| a central sheath, connected to the A tubules of peripheral doublets by radial spkes |
|
|
Term
For the structure of cilia and flagella, the doublets are interconnected to one another by an _____
___ at the tip, ___ at the base (cell body side)
A __ of the axoneme shows the continuous nature of the microtubules in contrast to other structures |
|
Definition
interdoublet bridge (nexin protein)
plus end ; minus end
longitudinal view |
|
|
Term
| The A and B tubules of the basal body elongate to form __ |
|
Definition
| the doublets of the cilium or flagellum |
|
|
Term
Cilia and flagella emerge from ___
–The growth of an axoneme occurs at the __ of microtubules.
–___ is the process responsible for assembling and maintaining flagella.
–IFT depends on the activity of both ___ and ___ microtubule movement.
|
|
Definition
basal bodies
plus ends
Intraflagellar transport (IFT)
plus end-directed (kinesin II) and minus end-directed (cytoplasmic dynein)
|
|
|
Term
| There are two rows of protein particles situated between the outer doublet microtubules and the flagellar plasma membrane. Each row of particles and its associated cargo of axonemal proteins are moved along the outer doublet microtubule by a motor protein. This consists of ___ which moves toward the flagellar base and ___ if the particles are moving toward the tip of the flagellum. |
|
Definition
| cytoplasmic dynein 1b and kinesin II |
|
|
Term
The machinery for ciliary and flagellar motion resides in the ___
___ is required for ATP hydrolysis, which supplies energy for locomotion |
|
Definition
axoneme
CIliary (axonemal) dynein |
|
|
Term
| ___ are heterogenous group of 70 proteins divided into 5 major classes. What are they? Describe some basic characteristics. |
|
Definition
Intermediate filaments (IFs)
•IFs classes I–IV are used in the construction of filaments; type V (lamins) are present in the inner lining of the nucleus.
•strong, flexible ropelike fibers that provide mechanical strength (neurons, muscles, epithelia)
•Found only in animals.
|
|
|
Term
| For the listed IF protein, what is the sequence type and primary tissue distribution: Keratin (acidic and basic), Vimentin, desmin, glial fibrillary acid protein (GFAP), peripherin, Neurofilament proteins (NF-L, NF-M, NF-H), Nestin, Lamin proteins (A, B, C) |
|
Definition
Keratin Acidic-I-Epithelia
Keratin Basic-II-Epithelia
Vimentin-III-Mesenchymal Cells
Desmin-III-Muscle
GFAP-III-Astrocytes
Peripherin-III-Peripheral neurons
Neurofilament protein L,M,H-IV-peripheral neurons, neurons of central and peripheral nerves
Nestin-IV-Neuroepithelial
Lamin proteins A,B,C-V-all cell types (nuclear envelopes) |
|
|
Term
| IFs radiate through the cytoplasm of a wide variety of animal cells and are often interconnected to other cytoskeletal filaments by thin wispy cross bridges. In many cells these cross bridges consist of an elongated dimeric protein called ___ that can exist in numerous isoforms. Each plectin molecule has a binding site for an intermediate filament at one end and depending ont he isform a binding site for another intermediate filament, microfilament, or microtubule at the other end. |
|
Definition
|
|
Term
The basic building block of IF assembly is thought to consist of __ formed by what?
Since the N and C termini point in opposite directions the tetramer and thus the IF, lack ___
__ tetramers join side by side to form a unit length of the filament
|
|
Definition
Basic building block is a rod-like tetramer formed by two antiparallel dimers (homodimers or heterodimers).
polarity
8 |
|
|
Term
| IFs are less sensitive to chemical agents than other types of cytoskeletal elements and are more difficult to solubilize. |
|
Definition
|
|
Term
| How is assembly and disassembly of IFs controlled? |
|
Definition
| phosphorylation and dephosphorylation |
|
|
Term
___ constitute the primary structural proteins of epithelial cells (including epidermal cells, liver hepatocytes, and pancreatic acinar cells). Provide protective barrier
IFs connect to ___ and ___
IFs include ___ which are the major component of the network supporting neurons |
|
Definition
Keratin filaments
hemidesmosomes and desmosomes
neurofilaments
|
|
|
Term
| Neurofilaments are composed of 3 distinct proteins what are they? |
|
Definition
|
|
Term
| IFs are seen to radiate throughout the cell being anchored at both the outer surface of the nucleus and the inner surface of the plasma membrane. Connections to the nucleus are made via proteins that span both membranes of the nuclear envelope and to the plasma membrane via specialized sites of adhesion such as desmosomes and hemidesmosomes |
|
Definition
|
|
Term
___ are composed of actin and are 8nm in diameter.
What do they provide for the cell? |
|
Definition
microfilaments
cell motility and intracellular movement(phagocytosis, cytokinesis, and vesicles |
|
|
Term
Using ATP actin polymerizes to form ___
The two ends of an actin filament have different ___ and ___ |
|
Definition
actin filaments
structural characteristics and dynamic properties |
|
|
Term
| In an actin filament structure, what is the overall shape and how many subunits for repeats? |
|
Definition
helical structure
Repeats every 13 subunits (36nm) |
|
|
Term
Adding myosin causes one end of the MF to appear ___ and the other to appear ___. Which end is plus or minus?
What does orientation of the arrowheads formed by myosin provide? |
|
Definition
pointed; barbed
Pointed= minus end
barbed end=plus end
information about direction of the microfilament movement |
|
|
Term
__ occurs after incorporation into filaments (analogous to GTP hydrolysis in microtubules).
Actin assembly/disassembly in vitro depends upon ___
In steady state, actin subunits are added to ___ and removed from the __
MIcrofilament cytoskeleton is organized by ?
|
|
Definition
Actin-bound ATP hydrolysis
concentration of actin monomers. High actin leads to growth at both ends.
plus end; minus end
controlling equilibrium spatially and temporally |
|
|
Term
| As long as the concentration of ATP actin monomers remains high subunits will continue to be added at both ends of the filament. As the monomers in the reaction mixture are consumed by addition to the ends of the filamentes the concentration of free ATP actin contiunes to drop until a point is reached where net addition of monomers continues at the plus end which has a higher affinity for ATP actin hbut stops at the minus end which has a lower affinity for ATP actin. As filament elongation continues the free monomer concentration drops further. Monomers continue to be added to the plus ends of the filaments but a net loss of subunits occurs at their minus end. As the free monomer concentratio nfalls a point is reached where the 2 reactions at opposite ends of the filaments are balanced so that both the lenghts and concentration remain constant. This is called __ |
|
Definition
|
|
Term
|
Definition
–Myosin is only known MF motor protein.
–Myosins move to + end (except myosin VI)
–All myosins share a characteristic motor head for binding actin and hydrolyzing ATP.
–The myosin tail is divergent. |
|
|
Term
| What are the 2 groups of myosins? |
|
Definition
Conventional (Type II) myosins
Unconventional myosins |
|
|
Term
| What are conventional (Type II) Myosins? |
|
Definition
–They generate force in muscles and some nonmuscle cells.
–Each myosin II is composed of six separate proteins: two heavy chains and four light chains.
–Heavy chain includes the head, neck, and long tail.
–S1 is name given to head/neck region (including light chains) that can be isolated after treatment with a protease.
Fibrous tail portion plays structural roleallowing the protein to form filaments. Filament is bipolar |
|
|
Term
| In Myosin II, all of the machinery required for motor activity is contained in what? What does the tail portion serve as? |
|
Definition
in a single head
Plays structural role allowing protein to form filaments |
|
|
Term
| Breifly describe Unconventional myosins. |
|
Definition
–17 types found to date (I, III-XVIII).
–Myosin I contains a single head.
–Myosin V is two-headed and is involved in organelle transport. Long neck allows long step size (36nm), or one MF helical repeat.
–Several unconventional myosins are associated with cytoplasmic vesicles and organelles.
•Myosin VI moves organelles from plus to minus end of actin filaments |
|
|
Term
| Vesicle transport primarily occurs along ___ but can occur along both __ and __ and can switch from ___ to ___ |
|
Definition
MTs
MTs and MFs
MTs to MFs |
|
|
Term
•A skeletal __ is a multinucleate cell as a result of fusion of ___ in the embryo.
•A single muscle fiber is large (10 to 100 um thick and can be more than 10 cm long) and highly organized.
•Each muscle fiber contains hundreds of cylindrical strands called __ |
|
Definition
muscle fiber; myoblasts
myofibrils
|
|
|
Term
| What are the levels of organization of skeletal muscle? |
|
Definition
Body Muscle
Muscle bundle and sheath
Muscle fiber and nuclei
Microfibril
Sarcomere(which contains Z line, I and A bands, and H zones) |
|
|
Term
•Each myofibril consists of a repeating array of ___
•Each sarcomere has a banding pattern that gives muscle fiber a ___appearance.
•What is the banding pattern?
•Sarcomere is bounded by ___.
•“Zee intelligent animals have muscle”
Muscle fibers show the banding pattern to be result of overlap between what 2 filaments. What are they composed of. Where are they found? |
|
Definition
sarcomeres.
striated
Banding pattern: light I band, dark A band. Within A band, lighter H zone and dark M band.
Z lines
•Thin filaments (mostly actin) found in I and A bands.
•Thick filaments (mostly myosin II) found in A and H bands.
|
|
|
Term
| Each thick filament is surrounded by ___ thin filaments and each thin is found in between ___ thick filaments |
|
Definition
|
|
Term
Skeletal muscle works by shortening fibers (___ decrease in total length)
___ bands remain constant in length
___ and ___ bands decrease in length
__ lines on both ends of sarcomere move inward
|
|
Definition
sarcomeres
A bands
H and I bands
Z lines |
|
|
Term
–Thin filaments contain actin as well as __ and ___
–Tropomyosin occupies the gap between two actin molecules and spans __ actin subunits in length.
–Troponin molecules are in contact with both __ and ___
–Thick filaments are mostly __, and form bipolar filaments with heads pointing to the ___. |
|
Definition
tropomyosin; troponin
7
actin and tropomyosin
myosin II ; Z line of the sarcomere |
|
|
Term
| Each thin filament consists of a helical array of actin subunits with rod shaped ___ molecules situated in the grooves and __ molecules spaced at defined intervals |
|
Definition
|
|
Term
•The third most abundant protein of skeletal muscles is __ (largest protein in nature).
•Titin starts at the __, and ends at the ___.
•Titin filaments are__and prevent the sarcomere from being pulled apart during __ (Z lines cant travel too far apart from each other).
•Titin also maintains ___ in their proper position. |
|
Definition
titin
M line, extend along the myosin filament ; Z line
elastic ; muscle stretching
myosin filaments
|
|
|
Term
| Titin molecules stretch from the end of the sarcomere at the ___ to the __ in the sarcomere center. Titin molecules are thought to maintain the thick filaments in the center of the sarcomere during contraction. The __ portion of the titin molecule contains spring like domains and is capable of great elasticity. The __ are thought to act like a molecular ruler by regulating the number of actin monomers that are allowed to assemble into a thin filament. |
|
Definition
Z line ; M band
I band
nebulin molecules |
|
|
Term
Molecular Basis of Contraction
–Myosin heads from a single thick filament contact about __ actin filaments.
–During contraction, myosin heads __, sliding the thin filaments over the thick filament (about 10nm per myosin). Head disassociates rapidly (non-processive).
–Myosin heads beat out of synchrony with each other, resulting in __ |
|
Definition
6
bend
several hundred nm total contraction. |
|
|
Term
–Energy released from __ induces a small conformational change within the head.
–Elongated myosin neck acts as a __, amplifying the movement 20 fold.
–Attached actin filament slides a much greater distance than would be possible with a simple head swivel. |
|
Definition
ATP hydrolysis
“lever arm”
|
|
|
Term
| During the power stroke, the neck of the Myosin molecule moves through a rotation of approximately 70 degrees which would produce a movement of the actin filament of approximately 10nm. |
|
Definition
|
|
Term
•The Energetics of Filament Sliding
–Energy is provided by ATPase activity in the __.
–ATP hydrolysis “activates” the __.
–Activated __ attaches to actin; release of __ initiates the power stroke.
–Release of bound ADP is followed by binding of another ATP, which induces the separation of ___ from ___.
–Absence of ATP prevents dissociation of myosin from actin, causing ___. |
|
Definition
myosin head
myosin
myosin-ADP-Pi ; Pi
myosin from actin
rigor mortis-stiffening of muscles that ensues following death
|
|
|
Term
| What are the steps of the actinomyosin contractile cycle |
|
Definition
Step 1: binding of ATP to a cleft in the myosin head causing the detachment of the head from the actin filament.
Step 2: Hydrolysis of the bound ATP
Step 3: This hydrolysis energizes the head causing it to bind weakly to the actin filament.
Step 4: Release of Pi causes a tighter attachment of the mosin head to the thin filament and the power stroke (moves thin filament toward center of the sarcomere)
Step 5: Release of ADP sets the stage for another cycle |
|
|
Term
–Contact between nerve and muscle is called the ___
–The linking of the nerve impulse to the shortening of the sarcomere is referred to as __
–Action potential in muscles is propagated into the cell interior by ___ |
|
Definition
neuromuscular junction.
excitation-contraction coupling.
transverse (T) tubules. |
|
|
Term
–T tubules terminate near the __, which stores __
–In a relaxed sarcomere, Ca2+ levels are high or low?
–An action potential opens __ in the SR, releasing __.
–Binding of Ca2+ to troponin causes a conformational change, shifting __ and exposing the ___. |
|
Definition
sarcoplasmic reticulum (SR) ; Ca2+.
low.
calcium channels; calcium ions
tropomyosin ; myosin binding site
|
|
|
Term
| When calcium levels rise, the interaction between __ and __leads to a movement of the __ from position b to position a which exposes the __ |
|
Definition
| calcium ; troponin ; tropomyosin ; myosin binding site on the thin filament to the myosin head |
|
|
Term
•Hereditary factors consist of __ and reside on ___.
•The collective body of genetic information in an organism is called the __
•Genome sequencing has revolutionized biology and is revolutionizing medicine. |
|
Definition
|
|
Term
•Mendel’s work became the foundation for the science of ___.
•He established the laws of inheritance based on his studies of __
|
|
Definition
|
|
Term
Characteristics of organisms are governed by units of inheritance called __
a)Each trait is controlled by two forms of a gene called __.
b)Alleles could be identical or nonidentical.
c)When alleles are nonidentical, the dominant allele can mask the ___ allele. |
|
Definition
|
|
Term
A reproductive cell (__) contains one gene for each trait.
a)__ arise by the union of male and
female gametes.
b) Two alleles controlling each trait are inherited; one
from each parent.
3. The pairs of alleles are separated (__) during gamete formation.
4. Genes controlling different traits segregate independently of each other (___). (The important exception: linked genes.) |
|
Definition
gamete
Somatic cells
segregated
independent assortment |
|
|
Term
–__ were first observed in dividing cells, using the light microscope.
–Chromosomes are divided equally between the two __during cell division.
–Chromosomes are doubled prior to cell division.
–Studies of ___ also helped narrow down the unit of inheritance.
•Cell body is much much smaller, but still contained an equal amount of chromosomes compared to__ |
|
Definition
Chromosomes
daughter cells
sperm cells
egg cells. |
|
|
Term
| Both the male and female gamete are seen to contain two chromosomes fusion of the sperm and egg nuclei (called __) in the egg cytoplasm (between e and f) produces a zygote containing four chromosomes. The second polar body shown in a is a product of the previous meiosis. |
|
Definition
|
|
Term
•Chromosomes as the Carriers of Genetic Information
–Chromosomes are present as pairs of __
–During meiosis, homologous chromosomes associate and form a __; then separate into different cells.
–Chromosomal behavior correlates with Mendel’s laws of ___ |
|
Definition
homologous chromosomes.
bivalent
inheritance |
|
|
Term
–Genes that are on the same chromosome do not assort ___
–Genes on the same chromosome are part of the same ___.
–The traits analyzed by Mendel fortuitously occur on different chromosomes (or are far apart enough to appear unlinked). |
|
Definition
independently
linkage group
|
|
|
Term
–Morgan was the first to use fruit flies in genetic research- Why did he use them?
–Morgan only had available__ flies, but, once he developed his first ___, it became a primary tool for genetic research.
–Mutations can arise spontaneously.
–Mutation was recognized as the mechanism for __ |
|
Definition
fast generation time, high number of progeny, small organism, inexpensive to maintain.
wild type; mutant
variation in populations and can lead to speciation. |
|
|
Term
| How many pairs of homologous chromosomes do drosophila melanogasters have? |
|
Definition
|
|
Term
| What are the recessive and dominant traits? |
|
Definition
Gray body and long wings= Dominant
short wings and black body |
|
|
Term
–Percentage of recombination between a particular pair of genes is ___
–Percentage of recombination between different pairs of genes can be different.
–The positions of genes along the chromosome (__) can be mapped.
–Frequency of recombination indicates __, and increases as distance __.
–Genes that are far enough apart on the same chromosome can appear __ to each other. |
|
Definition
constant
loci
distance ; increases
“unlinked”
|
|
|
Term
–Exposure to a sublethal dose of X-rays increases the rate of ___.
–Mutagenesis allows for the study of more genes in an organism more rapidly and completely.
–Modern genetics uses chemical (__) or insertional (__) mutagenesis.
–Mutagenesis Points to environmental hazards of radiation (X-ray, UV, radioisotopes) and chemicals in cancers, birth defects, etc. |
|
Definition
spontaneous mutations
ethyl methane sulphonate(EMS) or (transposons, transformed DNA)
|
|
|
Term
–Cells from the salivary gland of Drosophila have giant __
–Polytene chromosomes result from __
–Polytene chromosomes have been useful to observe__
–“Puffs” in polytene chromosomes allow visualization of __
–Other organisms have extra copies of DNA or extra chromosomes to facilitate more gene expression. |
|
Definition
polytene chromosomes.
extensive DNA duplication.
specific bands correlated with individual genes.
gene expression. |
|
|
Term
Polytene chromosomes show several thousand distinct, darkly staining bands. The bands have been identified as the loci of particular genes. The inset shows how polytene chromosomes consist of a number of individual DNA molecules. The stained bands on the chromosomes correspond to sites where the DNA is more tightly compacted.
Chromosome puffs are sites where DNA is being very actively transcribed |
|
Definition
|
|
Term
•___ is the genetic material in all organisms.
•The Structure of DNA:
–The __ is the building block of DNA.
What does it consist of?
•There are two different pyrimidines: ___ and ___
•There are two different purines: ___ and ___ |
|
Definition
DNA
nucleotide
•It consists of a phosphate, a sugar, and either a pyrimidine or purine nitrogenous base.
thymine (T) and cytosine (C).
adenine (A) and guanine (G) |
|
|
Term
•Nucleotides have a polarized structure where the ends are called __ and ___
•Nucleotides are linked into __:
–Sugar and phosphates are linked by __.
–Nitrogenous bases project out like stacked shelves. |
|
Definition
5’ and 3’
nucleic acid polymers
3’,5’-phosphodiester bonds |
|
|
Term
•Chargaff established rules after doing __ analysis:
What are the rules? |
|
Definition
base composition
–Number of adenine = number of thymine
–Number of cytosine = number of guanine
–[A] + [T] ≠ [G] + [C]
|
|
|
Term
•The Watson-Crick Proposal
–The DNA molecule is a __.
•DNA is composed of ___.
•The two chains spiral around each other forming a pair of ___hand helices.
•The two chains are __ they run in opposite directions.
•The ___is located on the outside of the molecule.___ make DNA highly negative.
•The bases are inside the helix and ___ to the long axis. |
|
Definition
double helix
two chains of nucleotides
right-
antiparallel:
sugar-phosphate backbone ; Phosphate groups
perpendicular
|
|
|
Term
–The DNA is a double helix
•The two DNA chains are held together by___
•The double helix is __ wide.
•Pyrimidines are always paired with purines.
•Only ___ and ___ pairs fit within double helix.
•Molecule has a ___ groove and a __ groove- useful for protein binding.
•The double helix makes a turn every __ residues.
•The two chains are __ to each other. |
|
Definition
hydrogen bonds between each base.
2 nm
A-T and C-G
major ; minor
10
complementary |
|
|
Term
•The Importance of the Watson-Crick Proposal
What 3 things does this proposal allow? |
|
Definition
1. Storage of genetic information- unique sequence identifier. DNA nucleotides can be in any order. A mutation is a change in DNA sequence.
2. Replication and inheritance- each strand can serve as a template for copying an identical new strand.
3. Expression of the genetic message. |
|
|
Term
| What three functions are required of the genetic material? |
|
Definition
1. DNA must contain the information that encodes inheritable traits
2. DNA must contain the information that directs its own duplication
3. DNA must contain the information that directs the assembly of specific proteins |
|
|
Term
| DNA that is more compact than its relaxed counterpart is called __ |
|
Definition
|
|
Term
–Underwound DNA is ___ supercoiled, and overwound DNA is __ supercoiled.
Negative supercoiling plays a role in allowing ___ |
|
Definition
negatively; positively
chromosomes to fit within the cell nucleus |
|
|
Term
–Enzymes called __ change the level of DNA supercoiling.
–Cells contain a variety of topoisomerases.
•___– change the supercoiled state by creating a transient break in one strand of the duplex.
•___– make a transient break in both strands of the DNA duplex. |
|
Definition
topoisomerases
Type I
Type II |
|
|
Term
enzyme cuts one of the strands of the DNA which rotates around the phosphodiester bond in the intact strand. The cut strand is then resealed.
In step 1, the enzyme is in the open comformation ready to bind the GDNA segment so named because it will form the gate through which the TDNA segement will pass. In step 2 the enzyme has undergone a conformationaly change as it binds the G segment. In steps 3 and 4 the enzyme binds a molecule of ATP, the G segment is cleaved and th T segment is passed through the open gate. THe bracketed stage represents the hypothetical intermediate carrying out the step in which the T segment is transported through the G segment/ At this stage both cut ends of te G segment are covalently bound to the enzyme. In step 5 the two ends of the G segment are rejoined and the T segment is released. ATP hydrolysis and release of ADP and Pi are proposed to occur as the starting state is regenerated. |
|
Definition
|
|
Term
| What are the 3 types of reactions that are catalyzed by topoisomerases? |
|
Definition
1. supercoiling relaxation reactions
2. knotting-unknotting reactions
3. catenation-decatenation reactions |
|
|
Term
__ is a rare event that occurs when offspring harbors more than one set of chromosomes from each parent.
How can this result?
•Many crop species are polyploid (some triploid, some tetraploid, most ancient tetraploid).
•Humans and other vertebrates are thought to have undergone How many genome duplications? |
|
Definition
Polyploidization (or whole genome duplication)
•Could result from duplicate chromosomes not separated in embryonic cells (more common in animals).
•Could result from hybrids from closely related parents (more common in plants).
2 |
|
|
Term
–Duplication and modification of DNA sequences is Much more common than polyploidy.
–__ occurs within a portion of a single chromosome.
–Duplication may occur by__between misaligned homologous chromosomes.
–Duplication has played a major role in the evolution of ___
–Duplication events provide raw material for __ |
|
Definition
Gene duplication
unequal crossing over
multigene families.
diversification of function in evolution.
|
|
|
Term
| Unequal crossing over between duplicated genes happens when there is an unequal sharing of genes between chromosomes |
|
Definition
|
|
Term
–The globin gene family includes ___, ___, and ___
–Ancestral forms have given rise to recent forms by duplication, rearrangement, and divergence.
Some sequences, called ___, resemble globin genes but are nonfunctional due to accumulated mutations or lack of gene expression. |
|
Definition
hemoglobin, myoglobin, and plant leghemoglobin.
pseudogenes |
|
|
Term
| Explain the steps to evolution for globin genes |
|
Definition
1. Begins with anesteral gene
2. Modern globin gene loses introns and exons from evolutionary time
3. These modern globin genes then diverge from other vertebrates prior to first duplication of globin gnee
4. These 2 copies then divergy by mutation to form 2 distinct globin types
5. There is then separation of genes due to the process of rearrangement
6. Each gene then underwent subsequent duplications and divergence
7. This generates the arrangement of globin genes that exists in humans |
|
|
Term
•“Jumping Genes” and the Dynamic Nature of the Genome
–Genetic elements are capable of moving within a chromosome called __
–Those mobile elements are called ___ |
|
Definition
transposition
transposable elements. |
|
|
Term
–Only certain sequences can act as __, and these insert into target sites randomly (though some tend to preferentially hop into nearby segments of DNA).
•It requires the enzyme __.
•Bacterial transposition occurs by excision of the ___, followed by ___. |
|
Definition
transposons
transposase
transposable element ; insertion
|
|
|
Term
| What are the steps to the "cut and paste" mechanism for bacterial transposons? |
|
Definition
1. 2 separate transposase subunits that bind to specific sequences at the ends of the transposon
2. 2 subunits then come together to form an active dimer
3. This dimer catalyzes a series of reactions leading to the excision of the transposon
4. The transposase-transposon complex then binds to a target DNA
5. The transposase catalyzes the reactions required to integrate the transposon into its new residence
|
|
|
Term
–Integration of the element creates a small duplication in target DNA, which serves as a __ to identify sites previously occupied by transposable elements.
–___ use an RNA intermediate which produces a complementary DNA via ____; viruses such as HIV use this mechanism to replicate their genome. |
|
Definition
“footprint”
Retrotransposons ; reverse transcriptase
|
|
|
Term
| pathways in movement of transposable elements (need info) |
|
Definition
|
|
Term
–At least 45% of the human genome consists of __.
–The vast majority (more than 99%) of transposons are ___.
–Active transposons can cause mutations and disease (e.g. hemophilia caused by a transposon hopping into blood clotting genes). |
|
Definition
transposable elements
inactive
|
|
|
Term
•The Role of Mobile Genetic Elements in Evolution
–Some moderately repeated sequences in human DNA (___ AND ___) are transposable elements (Alu and L1 are ___).
–__ is present in over a million copies. First originated in primates 60 million years ago.
–__ is present in about 500,000 copies.
–New copies of Alu and L1 are found in 1-2% of human births. |
|
Definition
Alu and L1 ; retrotransposons
Alu
L1
|
|
|
Term
•The Role of Mobile Genetic Elements in Evolution
–What is the traditional view?
–What is the new view?
–Transposons can rearrange the genome which in turn does what? |
|
Definition
transposons are DNA based parasites
transposons facilitate evolution by generating sequence diversity.
brings together different functional domains of proteins, making proteins with new combinations of functional domains.
|
|
|
Term
•The Role of Mobile Genetic Elements in Evolution
–Transposable element sequences also act as __, and can regulate new genes when transposed.
–Transposons have given rise to useful genes (e.g. telomerase and genes involved in antibody gene rearrangement). |
|
Definition
| gene regulatory sequences |
|
|
Term
•The genomes of hundreds of organisms have now been sequenced.
–Bacteria, 1995, Yeast, 1996; C. elegans, Drosophila, Arabidopsis around 2000. Easy to sequence, since they contain much less DNA than humans.
•Sequenced genomes revolutionized biology and biological research. |
|
Definition
|
|
Term
•In 2004 the “finished” version of the human genome was reported.
–Some regions are too repetitive to fully sequence.
–It contains about 20,000 genes, about the middle of the range among multicellular Eukaryotes, in 3.2 billion base pairs (3200 MB).
–Alternate splicing of messenger RNA may account for several proteins from one gene.
–Post-translational modifications also account for different protein functions. |
|
Definition
|
|
Term
•Comparative Genomics: “If It’s Conserved, It Must Be Important”
–In Humans, only 1.5% of DNA encodes for proteins. Does other DNA have a use?
–DNA that is not important for survival can mutate at much HIGHER FREQUENCIES!!
–Non-coding DNA that is similar among related organisms is considered to be important for survival.
–Much conserved DNA is in__ |
|
Definition
| gene regulatory elements or in chromosomal structural elements; others are completely unknown. |
|
|
Term
•The Genetic Basis of “Being Human”
–Studying how the human genome is different from other species should lead into insights about what makes us human.
–Humans and close relatives harbor the same genes, but some sequences evolved faster in humans.
–Differences in humans appear to be primarily due to changes in
___ and ___, sometimes extremely dramatic changes. This is
thought to be due to the rapid evolution of certain transcription
factors. |
|
Definition
| temporal and spatial gene expression |
|
|
Term
–___, the “speech gene” in humans, differs by only __ amino acids from chimps, but mutations in this gene in humans lead to inability to form muscular movements in speech.
–Another gene is __, which differs dramatically in humans from all other animals, and is thought to be involved in brain development.
–The gene ___ encodes the enzyme amylase (to digest starch) and its frequency is remarkably different between humans and chimps. |
|
Definition
|
|
Term
| Chimps only have one copy of the genome of AMY1 which is the starch digesting enzyme salivary amylase. Humans however have a number of copies. It varies within the human genome. One has 4 copies and the other has 10 copies. This is an example of ___ . This shows that the copy number of the AMY1 gene has been influenced by natural selection. |
|
Definition
|
|
Term
•Genetic Variation within the Human Species Population
–The genome varies among different individuals due to ___
–Example is the ABO blood type.
•DNA Sequence Variation
–The most common variability among humans is at the single nucleotide difference.
–These sites are called ___. Which alleles do the vast majority occur? |
|
Definition
genetic polymorphisms.
single nucleotide polymorphisms (SNPs).
A or G. |
|
|
Term
–Humans are, on average, different from each other at about 3 million base pairs, or 99.9% similar. (One out of every thousand base pairs is different). This is extremely low variability compared to other mammals, indicating how young our species is and how small the founding population was.
–Approximately 2 amino acid differences per gene |
|
Definition
|
|
Term
–Segments of the genome can change, and these changes may involve large segments of the DNA (these types of polymorphisms are called ___).
–Recent studies indicate that intermediate-sized variants are more common than previously thought.
–Changes involve ___, ___, ___, ___ and ___ |
|
Definition
structural variants
insertions, deletions, inversions, duplications, and transpositions(transfer of DNA from one chromosome to another) |
|
|
Term
Considering the Normal gene order given:
A B C D E F G H I
Explain what type of structural variants are taking place.
A B B C D E F G H
A B D E F G H I J
A B E D C F G H I
A B X Y Z C D E F |
|
Definition
Gene duplication
Deletion
Inversion
Insertion
|
|
|
Term
–Structural variations can occur in healthy individuals, but some have beneficial or detrimental consequences.
–Extra copies of ___ aids in starch digestion.
–Extra copies of the __ gene can lead to early Alzheimer’s. |
|
Definition
|
|
Term
•Until recently, the gene responsible for a disease was identified through traditional genetic linkage studies. Most suitable for diseases caused primarily by a single gene.
–For example, the Huntington’s disease gene, the CFTR gene for cystic fibrosis, etc.
•For diseases caused by multiple genetic changes,___ look for links between a disease and polymorphisms located in the genome. |
|
Definition
| genome-wide association studies |
|
|
Term
–____ are Useful for diseases like heart failure, diabetes, asthma, depression, cancer, etc.
–Can identify a large number of genes, particular alleles of which increase susceptibility (but do not always lead to the disease, because of other genetic factors or environmental factors). |
|
Definition
| Genome wide association studies |
|
|
Term
•Several contributing genes have now been identified for some diseases.
–In most cases, the increased risk of any particular allele is very slight.
•___, rather than nucleotide changes, also play a role.
•Continued progress in genome sequencing technologies and expression analysis is predicted to dramatically impact medicine. |
|
Definition
|
|
Term
•A special case: cancer genome sequencing
–Most cancers are due to accumulated mutations.
–Soon it will be cost-effective to sequence the genome from an individual’s normal (healthy) cells, and compare to the sequence of the genome of cancerous cells.
–Determining which genes are mutated in the cancerous cell can lead to specific drug treatments. |
|
Definition
|
|
Term
•Genes store information for producing all cellular ___.
•Early observation suggested a direct relationship between genes and proteins.
–Garrod studied the relationship between a specific gene, a specific enzyme, and a metabolic condition (___).
–Beadle and Tatum formulated the hypothesis ___ by isolating ___ mutants that can’t grow on minimal media. |
|
Definition
proteins
alcaptonuria
“one gene–one enzyme” ; Neurospora |
|
|
Term
| What is the Beadle Tatum experiment? |
|
Definition
| Spores were irradiated to induce mutations and allowed to grow into colonies in tubes containing supplemented medium. individual spores produced by the colonies were then tested for their ability to grow on the minimal medium. Those that failed to grow were mutants and the task was to identify the mutant gene. A sample of mutant cells was found to grow in the minimal medium supplemented with vitamins, but would not grow in medium supplemented with amino acids. This observation indicates a deficiency in an enzyme leading to the formation of a vitamin. The growth of these same cells in minimal medium supplemented with one or another of the vitamins indicates the deficiency resides in a gene involved in the formation of panthothenic acid. |
|
|
Term
•Beadle and Tatum’s hypothesis was later modified to __
•Alternative splicing means what?
•Mutation in a single gene can cause a single substitution in an amino acid sequence of a single protein, sometimes with dramatic consequences. |
|
Definition
“one gene–one protein"
many varying proteins can be formed from a single gene
|
|
|
Term
•An Overview of the Flow of Information through the Cell
–___ is an intermediate between a gene and a polypeptide.
–___ is the process by which RNA is formed from a DNA template.
–___ is the process by which proteins are synthesized in the cytoplasm from an mRNA template.
–Often expressed as __-->__-->___ (__). |
|
Definition
Messenger RNA (mRNA)
Transcription
Translation
DNA->RNA->Protein (central dogma) |
|
|
Term
| The DNA of chromosomes located within the nucleus contains the entire store of genetic information. Selected sites on the DNA are transcribed into ___ which are processed into ___. The messenger RNAs are transported out of the nucleus into the cytoplasm. where they are translated into __ by ribosomes that move along the mRNA. Following translation, the polypeptide folds to assume its native conformation. |
|
Definition
pre mRNAs
messenger RNAs
polypeptides |
|
|
Term
•There are four classes of RNA in a cell: what are they?
•rRNAs do what?
___ are required to translate information in the mRNA code into amino acids. |
|
Definition
mRNA, ribosomal RNA (rRNA), transfer RNA (tRNA) and small regulatory RNAs that were recently discovered.
recognizes other molecules, provide structural support, and catalyzes the chemical reaction in which amino acids are linked to one another. Structure is based on paring of stretches of complementary regions.
•tRNAs |
|
|
Term
| Base paired regions typically form double stranded stems which are connected to single stranded loops. Unlike DNA which consists exclusively of standard watson crick base pairs, RNAs often contain ___ and ___. These unorthodox regions of the molecule serve as recognition sites for proteins and other RNAs, promote RNA folidng and help stabilize the structure of the molecule |
|
Definition
| nonstranded base pairs ; modified nitrogenous bases |
|
|
Term
•___ are responsible for transcription in both prokaryotes and eukaryotes.
•These enzymes incorporate nucleotides, one at a time, into a complementary strand of RNA from a ___.
–The ___ is where the enzyme binds prior to initiating transcription.
–The enzyme requires the help of ___ to recognize the promoter. |
|
Definition
DNA-dependent RNA polymerases (or RNA polymerases)
DNA template
promoter
Transcription factors
|
|
|
Term
| The polymerase covers approximately 35 base pairs of DNA, the transcription bubble composed of single stranded (melted) DNA contains about 15 base pairs and the segment present in a DNA-RNA hybrid includes about 9 base pairs. The enzyme generates overwound DNA ahead of itself and underwound DNA behind itself. |
|
Definition
|
|
Term
•The newly synthesized RNA chain grows in a __ direction antiparallel to the DNA.
–RNA polymerase must be __ – remain attached to DNA over long stretches, even up to 2000kb, but RNA polymerase must also be able to move from nucleotide to nucleotide. 20-50 nucleotides per second.
•Nucleotides enter the polymerization reaction as ___
•The reaction is driven forward by the hydrolysis of a pyrophosphate: What is the reaction? |
|
Definition
5’ to 3’
processive
triphosphate precursors.
PPi à 2Pi
|
|
|
Term
| In the act of transcription elongation, the downstream DNA lies in a groove within the polymerase, calmped by a pair of jaws formed by the two largest subunits of the enzyme. The DNA makes a sharp turn in the region of the active site, so that the upstream DNA extends upward. The nascent RNA exits from the enzymes active site though a separate channel |
|
Definition
|
|
Term
| Chain elongation results folloing the attach by the 3' OH of the nucleotide at the end of the growing strand on the 5' alpha phosphate of the incoming nucleoside triphosphate. The pyrophosphate relased is subsequently cleaved, which drives the reaction int he direction of polymerization. The geometry of base pairing between the nucleotide of the template strand and the incoming nucleotide determines which of the four possible nucleoside triphosphates is inforporated into the growing RNA chain at each side. |
|
Definition
|
|
Term
•Once polymerase has finished adding nucleotides, the DNA-RNA hybrid completely dissociates and the ___reforms.
•Transcription is subject to ___, ___, and ___
•There are two enzymatic activities of RNA polymerase: what are they? |
|
Definition
DNA double helix
pauses, errors, and backtracking.
digestion of incorrect nucleotides and polymerization.
|
|
|
Term
•Transcription in Bacteria
–There is only one type of RNA polymerase in prokaryotes: what is it composed of and what is it tightly associated to form?
–Transcription-competent cells also have a ___ attached to the RNA polymerase before attaching to DNA. What does this allow? |
|
Definition
five subunits associated to form a core enzyme. This will randomly transcribe DNA in vitro.
sigma factor ; This allows the polymerase to bind to promoters and transcribe only the intended DNA.
|
|
|
Term
| In the absence of the sigma factor what happens? |
|
Definition
| the core enzyme does not interact with the DNA at specific initiation sites. When the core enzyme is associated with the sigma factor, the complete enzyme is able to recognize the bind to the promoter regions of the DNA, separate the strands of the DNA double helix and initiate transcription at the proper start sites The sigma factor dissociates from the core enzyme which is capable of transcription elongation. |
|
|
Term
•Bacterial promoters are located ___ from the site of initiation.
–Two conserved regions: –what are they?
•Differences in the DNA sequences at both the –35 element and the Pribnow box may regulate ___
•Termination in bacteria can either require a ___ protein or may reach a __ |
|
Definition
upstream
35 element (consensus sequence TTGACA) and Pribnow box (consensus sequence TATAAT).
gene expression.
rho factor ; terminator sequence without rho.
|
|
|
Term
•Transcription and Processing in Eukaryotic Cells
–There are at least __ types of RNA polymerases in eukaryotes.
•Most rRNAs are transcribed by __.
•mRNAs and most small regulatory RNAs are transcribed by RNA __.
•tRNAs and a few other small RNAs are transcribed by RNA ___.
•In plants, some siRNAs are transcribed by___ |
|
Definition
3
RNA polymerase I
polymerase II
polymerase III
RNA polymerase IV and V (V is found only in Angiosperms).
|
|
|
Term
| For the Enzymes RNA polymerase I, II, III, IV, and V describe which RNAs are synthesized. |
|
Definition
RNA polymerase I : larger rRNAs (28s, 18s, 5.8s)
RNA polymerase II: mRNAs, most small nuclear RNAs (snRNAs and snoRNAs), most microRNAs, and telomerase RNA
RNA polymerase III : small RNAs, including tRNAs, 5S rRNA, and U6 snRNA
RNA polymerase IV, V (plants only) : siRNAs |
|
|
Term
•____ regulate the activity of RNA polymerases.
•Newly transcribed RNAs are processed.
–A __ is the initial RNA molecule synthesized.
–A __ is the DNA segment corresponding to a primary transcript.
–A variety of small RNAs are required for RNA processing. |
|
Definition
Transcription factors
primary transcript (or pre-RNA)
transcription unit
|
|
|
Term
•A eukaryotic cell may contain millions of ribosomes.
•The DNA sequence encoding rRNA are called __, and is typically clustered in the genome as hundreds of repeats.
•5 clusters in humans, all on different chromosomes.
•In nondividing cells, rDNA are clustered in the __, where ribosomes are produced. |
|
Definition
|
|
Term
| What are the three distinct nuclear regions that can be distinguished morpholigically? |
|
Definition
| The bulk of the nucleolus consists of a granular component (gc) which contains ribosomal subunits in various stages of assembly. Embedded within the granular region are fibrillar centers (fc) that are surrounded by a more dense fibrillar component (dfc) |
|
|
Term
–rRNA genes are arranged __.
–rRNA transcription has a __ pattern under TEM.
–Proteins that convert rRNA precursors into mature rRNA become associated with __ during transcription.
–The ___ separates transcription units in a ribosomal gene cluster. |
|
Definition
in tandem
“Christmas tree”
pre-rRNA
nonstranscribed spacer
|
|
|
Term
| Each of the 100 or so fibrils emerging from the DNA as a branch of a christmas tree is a nascent rRNA transcript caught in the act of elongation. The dark granule at the base of each fibril, visible in the higher magnification photograph is the RNA polymerase I molecule synthesizing that transcript. |
|
Definition
|
|
Term
| Nascent RNA transcripts contain associated particles. These particles consist of RNA and protein that work together to convert the rRNA precursors to their final rRNA products and assemble them into ribosomal subunits. What is an area of the ribsosomal gene cluster which is not transcribed called? |
|
Definition
|
|
Term
–rRNA contains large numbers of __ and __. Changes are made __.
–A single primary transcript (___) is spliced into three rRNAs: __, __, and __ (The __ transcript is synthesized outside the nucleolus.)
–Only sections of the pre-rRNA that will reside in mature rRNAs are modified. |
|
Definition
methylated nucleotides and pseudouridine residues ; posttranscriptionally
pre-rRNA ; 28S, 18S, and 5.8S. ; 5S
|
|
|
Term
–Processing of pre-rRNA is guided by __
–snoRNAs are packaged with many proteins into __
–The U3 snoRNA removes the __ of the transcript. |
|
Definition
small, nucleolar RNAs (snoRNAs).
snoRNPs (small, nucleolar ribonucleoproteins).
5’ end |
|
|
Term
•The Role of snoRNAs
–C/D box snoRNAs methylate the __.
–H/ACA box snoRNAs convert __ to ___.
–There are about 200 different snoRNAs in humans, each one specific for one nucleotide of the rRNA that is changed (over 100 methylated riboses and about 95 uridines converted).
–Catalysis involves a double-stranded RNA step between the __ and the __. |
|
Definition
ribose group
Uridines to pseudouridines
rRNA ; snoRNA sequence |
|
|
Term
–The __ genes are located outside the nucleolus around the genome.
–It is transcribed by __, which can use an __ rather than a __ used by other polymerases. |
|
Definition
5S rRNA
RNA polymerase III ; internal promoter ; 5' promoter |
|
|
Term
–tRNAs are used in protein synthesis to match the __ to an amino acid.
–tRNA genes are located in small clusters scattered around the genome.
–Number of tRNA genes varies among species; humans have about 1300. |
|
Definition
|
|
Term
–tRNAs have promoter sequences within the coding region of the gene, and are transcribed by __
–During processing, the tRNA precursor is trimmed and numerous bases must be modified.
–One enzyme that trims tRNA is an endonuclease called __, which is composed of both protein and RNA subunits. |
|
Definition
RNA polymerase III.
ribonuclease P |
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Term
•mRNAs serve as the template for __.
•The precursors of mRNAs are represented by diverse RNAs called __.
–hnRNAS are found only in __.
–hnRNAs have large ____
–hnRNAs are __ and are processed or degraded after a very short time compared to other RNAs. |
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Definition
protein synthesis
heterogeneous nuclear RNAs (hnRNAs)
the nucleus
molecular weights.
transient (do not last long) |
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Term
•The Machinery for mRNA Transcription
–___ transcribes all mRNAs in eukaryotes, and is highly conserved.
–RNA polymerase II is assisted by __ to form the__
–The critical portion of the promoter lies 24-32 bases upstream from the initiation site, and contains the __
–The preinitiation complex of GTFs and polymerase assemble at the __. |
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Definition
RNA polymerase II
general transcription factors (GTFs)-present when gene is expressed ; preinitiation complex (PIC).
TATA box (TATAAA).
TATA box |
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Term
| TATA box is upstream of transcription initiation site. What is the TATA box for the following animals: Chicken ovalbumin, Rabbit Beta globin, and mouse Beta globin major? |
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Definition
Chicken: TATATAT
Rabbit: CATAAAA
Mouse: TATAAGG |
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Term
•The preinitiation complex assembly starts with the binding of the __ to the promoter.
•(Note that the majority of genes lack a TATA box, not always conserved, but still utilize TBP.)
•TBP is a subunit of __
•When TBP binds to the promoter, it binds in the __, and causes a conformation change in DNA. |
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Definition
TATA-binding protein (TBP)
TFIID (transcription factor for polymerase II, fraction D).
minor groove (different because most bind to major groove because there is more room) |
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Term
| When TBP binds it causes a bend or twist in DNA |
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Definition
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Term
•Step 1: Binding of __ sets the stage for the assembly of the complete PIC. First thing that binds!!
•Step 2:The three GTFs (__ of ___, ___,and ___)bound to the promoter allows the binding of RNA polymerase with its attached TFIIF.
•Step 3:Two more GTFs, ___ and ___, bind next and activate the polymerase. |
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Definition
TFIID
TBP of TFIID, TFIIA, and TFIIB
TFIIE and TFIIH
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Term
| Initiation of transcription from a eukaryotic polymerase II promoter |
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Definition
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Term
•__ is only GTF that has enzymatic activity,__ in one subunit and __ (to unwind DNA) in two others.
•__ and some other GTFs are left behind at the promoter once transcription starts.
•As long as TFIID remains bound to the promoter,what is allowed? |
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Definition
TFIIH = last one to bind ; protein kinase; DNA helicase
TFIID.
additional RNA polymerases may be able to attach for additional rounds of transcription.
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Term
•Generalized transcription factors alone can promote a low level of transcription __.
•__ determine whether or not a preinitiation complex assembles at a particular promoter, and determine the rate at which the polymerase initiates new rounds of transcription.
•Transcription termination for RNA Polymerase II is not understood. |
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Definition
in vitro
Specific transcription factors
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Term
The Structure of mRNAs: Messenger RNAs share certain properties
–They each code for a __.
–They are found in the ___.
–They are attached to __ when translated.
–Nearly all have __.
–Eukaryotic mRNAs have modifications at their __end (__) and a __end (__). |
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Definition
specific polypeptide
cytoplasm
ribosomes
noncoding segments.
5’ ; methylguanosine cap; 3' ; poly (A) tail |
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Term
methylguanosine is added at the __ end and polyA tail is added to the __ end
They surround coding region |
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Definition
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Term
–The difference between hnRNA and mRNA provided early clues about RNA processing. Have more introns
–Eukaryotic genes contain __which are missing from mature mRNAs.
–Genes with intervening sequences were called __ |
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Definition
intervening sequences
split genes.- split into several regions along chromosome |
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Term
| What happens in processing of a split gene |
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Definition
| these split genes are spliced out and the coding regions are spliced together into mature mRNA |
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Term
| introns can be of varying lengths. Some introns can be large. They are spliced together to make a mature mRNA. |
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Definition
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Term
•The parts of the split gene that contribute to the mature mRNA are called __.
•The intervening sequences are called __.
•The discovery of genes with introns led scientists to investigate how these genes were able to produce mRNAs lacking these sequences. |
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Definition
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Term
| some genes can have only one intron, some can have none. |
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Definition
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Term
main steps: addition of guanosine cap, poly a tail, splicing of introns.
–RNA transcripts become associated with __ and __ as they are synthesized.
–During processing, a ___ and ___ are added..
–Intervening sequences are removed and exons are connected by RNA splicing.
All processing steps occur in the__ during or immediately after transcription. They are then transported to the ___ |
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Definition
proteins ; ribonucleotides
5’methylguanosine cap and 3’poly(A) tails are added
nucleus ; cytoplasm |
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Term
| as gene is transcribed it is being tanscribed multiple times at once. Proteins are added to the transcript while it is being synthezised. |
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Definition
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Term
Once the 5' end of tan mRNA precursor has been synthesizee, several enzyme activities act on this end of the molecule. What are the steps and enzymes?
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Definition
Step 1: RNA triphosphatase cleaves the gamma-Bphosphoanhydride bond of nascent mRNA molecule and releases a free phosphate group. Converts 5' terminus to a diphosphatate
Step2: Guanylyltransferase then adds a guanine residue in a reverse orientation by means of 5' to 5' linkage.
Step 3: different methhyl transferases add a methyl group to the terminal guanosine cap and to the ribsose of the nucleotide that had been at the end of the nascent RNA
A protein complex calle dCBC binds to the completed cap. A very different series of events occurs at the 3' end of the premRNA where a large protein compelx is assembled/ First an endonuclease cleaves the primary RNA transcript generating a new 3' end upstream from the origianl 3' terminus. In steps a-c poly A polymerase adds adenosine residues to the 3' end without involvement of of a DNA template. A typical mamalian mRNA contains 200 to 250 adenosine residues in its compelted poly A tail |
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Term
methylguanosine cap: When is it added. What does it protect. What does it aid?
3’ poly(A) tail: What sequence triggers it. How many adenosines? what does it aid?
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Definition
-Added very early during transcripton
-Protects from exonucleases
-Aids in export out of nucleus
-Aids in initiating translation
-AAUAAA sequence triggers it
-about 250 adenosines
-also aids in export and translation
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Term
•RNA Splicing: Removal of Introns from a Pre-mRNA
–Breaks are introduced at the 5’ and 3’ endsof an intron (__).
–Must be precise: loss of a single nucleotide can render the protein NON FUNCTIONAL!!.
–Sequences between exon-intron boundaries are highly conserved. In mammals, sequences most commonly found at the boundaries are __ at the 5’ end and __ at the 3’ end.
– |
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Definition
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Term
| Nucleotide sequences at the splice sites of pre-mRNAs. What are the splice sites at each end? |
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Definition
| GGU at 5' and AGG at 3' with polypyrimidine tract |
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Term
•The mechanism of RNA splicing has led to the study of RNA enzymes, or __.
•RNA splicing is thought to have evolved from __.
An example of a self-splicing intron is the __, found in mitochondria, chloroplasts, and select bacteria and archaea |
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Definition
ribozymes
self-splicing RNAs
group II intron
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Term
•The pre-mRNA is not capable of self-splicing, and requires__
•As each hnRNA is transcribed, it becomes associated with proteins to form a __.
•Processing occurs as each intron becomes associated with a RNA-protein complex called a __.
•The spliceosome consists of __ |
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Definition
small nuclear RNAs (snRNAs).
hnRNP
spliceosome
small nuclear ribonucleoproteins (snRNPs).
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Term
•Removal of an intron requires: What 2 things?
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Definition
1. Several snRNP particles.
2. Each snRNP contains an Sm family protein and dozen or more unique proteins |
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Term
| RNAs are required for splicing of messenger RNAs |
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Definition
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Term
| Splicing occurs in certain order. it is not random. if gene has introns those introns are spliced out in the same order. That is why there is different bands. |
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Definition
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Term
–The idea of an __suggests that RNA was the earliest molecule to both store information and catalyze reactions. (Functions are now separated between protein and DNA.)
–RNA splicing via spliceosomes could have evolved from __.
–__ of “genetic modules” could have played a role in the evolution of many genes.. Exons allow gene functions to allow different gene functions
–Alternative splicing-any type of splicing that does not occur the same.. can greatly increase the number of different proteins present. |
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Definition
"RNA world”
self-splicing RNAs
Exon shuffling
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Term
__ results in the destruction of some mRNAs.
•This phenomenon results in __
•RNAi occurs when a double-stranded RNA shares the same sequence as the __.
•___ or ___ can trigger RNAi. |
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Definition
•RNA interference (RNAi)
post-transcriptional gene silencing (PTGS).
target mRNA
Production or injection of double stranded RNA (dsRNA) |
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Term
RNAi is part of a broader phenomenon of ___, in which small RNAs inhibit gene expression in various ways.
What are the steps involved in RNAi?
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Definition
RNA silencing
–dsRNA is cleaved into small interfering RNAs (siRNAs) by an enzyme called Dicer.
–The small dsRNAs join a complex named RISC that removes the passenger strand and binds siRNA to a target RNA. This results in destruction of the target RNA. |
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Term
•RNAi may have evolved as a defense against __ and/or ___
•Used in plants and invertebrate animals, so RNAi is used especially in these organisms but vertebrates can use an immune system (although RNAi machinery is present in vertebrates).
•Suitable for defense: how does it work? |
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Definition
viruses and/or transposons.
can transcribe from opposite strand in order to make a complementary RNA strand. |
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Term
•MicroRNAs (miRNAs)-used for normal development and growth
–Are derived from __ precursor RNAs that contain complementary sequences that allow them to fold back to form a region of __.
–miRNAs are encoded as __ at various locations around the genome, unlike siRNAs.
–miRNAs occur naturally and are used in the course of normal growth, development, and metabolic processes. |
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Definition
single-stranded ; double stranded RNA (dsRNA)
separate (small) genes |
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Term
•MicroRNAs (miRNAs)
–The pseudo dsRNA of a miRNA is cleaved by __ to generate a __.
–This small dsRNA joins a __ and the __ strand is removed, just like in siRNA.
–The single-stranded miRNA binds to a complementary region on an mRNA and inhibits translation of the message or (in plants) degrades it.
–A broad range of genes are naturally regulated by miRNAs. |
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Definition
Dicer ; pre-miRNA
RISC complex ; passenger |
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Term
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Definition
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Term
•Strategies for using RNAi to combat disease are being developed against a VERY broad range of cancer, viruses, and genetic disorders.
•Although the technique has shown amazing promise, some obstacles remain:
what are they? |
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Definition
–Delivering genes for siRNAs can lead to complications.
–Viral genes mutate rapidly, making some siRNAs ineffective for treatment against viral diseases. |
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