Exam 2

Lecture 18

Three major structural elements of the cytoskeleton

- microtubules, microfilaments and intermediate filaments
For microtubules and the actin filaments you need to know their perspective monomers, how they assemble,
the main functions of these structures
- G-actin monomers can polymerize reversibly into filaments with a lag phase and elongation phase, similar
to tubulin assembly, F-actin filaments are composed of two linear strands of polymerized G-actin would into helix, all
the actin monomers in the filament have the same orientation
- microtubules form by the addition of tubulin dimers at their ends, GTP and MG2+ are essential for
polymerization, microtubule assembly in vitro depends on concentration of tubulin dimer, the tubulin concentration at
which MT assembly exactly balanced by disassembly is called critical concentration
- actin is the protein block for the cell
How the cytoskeleton is organized and where in the cell you find different type of cytoskeleton structures
(e.g. mitotic spindle, MTOC, for microtubules and stress fibers or actin bundles etc and for microfilaments)
- The cytoskeleton is organized by having microtubles, intermediate filaments, and
microfilaments. Within these structures microtubules contain vesicle transporters. within the microfilaments
there is filapodia and lamellipodia which help with cell transport and signaling
Be able to name at least one binding protein associated with the actin microfilaments and the microtubules
and their role in cytoskeletal remodeling
- MAPs, microtubule-asssociated proteins, binds at regular intervals along a
microtubule wall, allowing for interaction with other cellular structures and filaments
- MAP called Tau causes MT’s to form tight bundles of axons, MAP2 promotes the formation of looser
bundle in dendrites
Understand how drugs acting on the cytoskeleton can affect cell function (e.g. antimitotic drugs)
- drugs can affect assembly and stability of microtubule
- assembly inhibitors:
- colchicine: binds to tubulin monomers, inhibiting their assembly into MTs
promoting MT
- nocodazole: inhibits MT assembly and it effects are more easily reversed than those of colchicine
- disassembly:
taxol: binds tightly to microtubules and stabilize them
- these drugs are antimitotic because they interfere with spindle assembly and thus inhibit cell division, they
are useful for cancer treatment because cancer cells are rapidly dividing and susceptible to drugs that inhibit mitosis,
while taxol as an opposite effect on tubulin assembly it is also used for cancer treatment especially for breast cancer,
it causes dividing cells to arrest in mitosis

Lecture 19

What are the different type of motility or movement?

- movement of a cell or organism through the environment
- movement of the environment past or through the cell
- muscle contraction
Can you describe what motor proteins are and name the three families of motor proteins?
- motor proteins are molecular motors that use ATP hydrolysis to move along
cytoskeletal filaments within the cell. They fulfill many functions within biological systems, including
controlling the sliding of filaments in muscle contraction and mediating intracellular transport along bipolymer filament
tracts.
- myosin, kinesin, dyenin
Remember that motor proteins work in concert with the cytoskeleton
Be able to understand and describe fast axonal transport in neurons and muscle contraction.
- fast axonal transport is protein produced in the cell body are transported to the nerve ending in this
process
- anterograde axonal transport is when kinesin-I is involved in ATP-dependent transport towards the plus
end
- retrograde axonal transport is when cytosplasmic dynein moves particles in the opposite direction
- muscle contraction is a microfilament-based motility when the thin actin and thick myosin filaments slide
past each other. It is generally assumed that this process is driven by cross-bridges which extend from the myosin
filaments and cyclically interact with the actin filaments as ATP is hydrolysed.
Where does energy come from?
- mitochondria
What is processivity?
- molecular motors undergo cycles of ATP hydrolysis, ADP release and acquistion of new ATP
For muscle contraction remember that while ATP is necessary, no contraction will happen unless calcium
concentration increases and activates tropomyosin-troponin complex
Annotate slide 19,27,29,30

Lecture 20

Be sure to know the different type of cell junctions, their functions and the major proteins they are made of
(e.g. can you tell which junctions these proteins are associated with: cadherins, claudins, integrins or
connexins?)
- tight junctions: create an impermeable seal between cells “water tight seal” , major protein is claudin
- gap junctions: allow direct chemical and electrical communication between cells by allowing passage of
small molecules and ions , major proteins are connexons
- adhesive junction: includes desmosomes which anchor the cell to cell adhesion, major protein is cadherins
Can you describe the distinction between heterophilic and homophilic interactions?
- heterophilic interactions: cells with different receptors interact
- homophilic interactions: cells with identical receptors on their surfaces interact with one another
Be able to describe how you would experimentally test if two cell types are connected via gap junctions in
cell culture (e.g. use dyes)

Lecture 21

Understand that different type of ECM are found in different tissue

- bone
- cartilage
- connective tissue
While highly variable the ECM have similar organization and contain three major types of proteins
- structural proteins, protein-polysaccharide, adhesive glycoproteins
Slide 5 summarizes the lecture
You should know the structure and function of these majors ECM components (e.g. collagen fiber made of
fibrils and important for high tensile strength of a tissue
Can you describe how do cells attach to the ECM?
- it can be focal adhesion, connection the ECM to actin filaments of the cell, and hemidesmosomes
connecting the ECM to intermediate filaments such as keratin
What are the two major protein families involved?
- adhesive glycoproteins

Lecture 22

Can you describe experiments from Oswald Avery and colleagues with r and s bacteria strain?
- s strain caused a fatal infection when introduced into mice, r strain was unable to do so
- they followed up the experiment by Griffith by trying to determine what the
transforming substance was , they fractioned extracts of the s-strain bacteria and tested destroyed
separately macromolecule classes.
And Hersey and Chase’s experiment phages? What the purpose of these experiments?
- they showed that DNA is the genetic material of viruses, bacteriophages are viruses that infect bacteria,
- phage T2, T4 and T6 are the best studied
Would you be able to design an experiment similar to Avery’s one but using bacterial transformation and
antibiotic resistance instead of bacterial virulence on mice (slide 29)?

Lecture 23

Know the DNA is compacted in cells

- DNA is compacted with the use of histones which causes the DNA to become coiled into chromatin. Two
types include euchromatin and heterochromatin. Euchromatin is loosely pack and used for transcription, and
heterochromatin is tightly packed and not used for transcription.
What are the names of the different form of genomic DNA (e.g. nucleosomes, chromatin fibers,
heterochromatin/euchromatin and chromosomes)
- Constitutive vs Facultative
Facultative is when genes are silence through histone deacedylation
It does not have repeats
What are the key proteins allowing DNA packaging (e.g. histones)
- Constitutive is attached to nuclear membrane
H1 (special one) H2a H2b H3 H4
How are these proteins dynamically regulated to remodel chromatin?
Which enzymes enable this regulation =HMTs, HATs, HDACs (know their full names)
What is the difference between facultative and constitutive heterochromatin?
Which par of chromosomes are composed of constitutive heterochromatin (=centromeres and telomeres)
What are their respective roles?
Comparing DNA denaturation/renaturation properties as well as genome sizes of eukaryotes and
prokaryotes, scientists discovered that eukaryotic genomes contain large amounts of repeated DNA
sequences.
Can you tell by looking at the graph in slide 39?
Where are these DNA repeats found? (centromeres and telomeres but also all over the genomes. we saw in
lecture 25 that trinucleotides repeats can be a source of DNA damage and disease)

Homework Questions:
● Homework 1
1) Robert Hooke coined the term cell when studying thin slices of cork. These ________ were the
first cells observed because ________.
dead plant cells; the thick cells walls did not require high resolution or magnification to view
 2) Cell biology emerged from which of the following fields of biology?
biochemistry, cytology, and genetics

3)Which of the following statements does NOT correctly validate the three strands that compose
modern cell biology?
All of the other available answer choices validate the relationships between the three strands that
compose modern cell biology.

4) Which type of microscopy has the greatest resolving power?

electron microscopy

5) Which of the following is an application of immunofluorescence microscopy?

Identifying which organelle or cellular compartment contains a particular protein.

6)Gregor Mendel was most influential in which field of biology?

Genetics

To which of the following do Mendel's observations relate?

Heredity

In 1880, Walther Flemming identified ________, threadlike bodies seen in dividing cells.
Chromatin

Koo¨llicker describes "sarcosomes" (now called mitochondria) in muscle cells (1857).

Cytological

Hoppe-Seyler isolates the protein hemoglobin in crystalline form (1864).

Biochemical

Cytological strand
● Light microscopy/electron microscopy
● Transmission electron microscopy/scanning electron microscopy

Biochemical strand
● Centrifugation/ultracentrifugation
● Chromatography/electrophoresis

Genetic strand
● Nucleic acid hybridization/DNA sequencing
● Sequencing of a genome/bioinformatics

Which of the following statements is false?

All cells have a membrane-bound nucleus.

You are studying the response of macrophages infected with the intracellular bacterium Brucella,
specifically by examining which gene products are being expressed. You would be studying the
macrophage ________ to obtain this information.
transciptome
 Many oils will not dissolve in water. Water is polar.

Many salts dissolve in water. Water is a good solvent.

Most people get chilled immediately after taking a shower. Water has a high heat of

vaporization.

On cold days, the water temperature is often warmer than the surrounding air. Water has a high

specific heat.

A dime can be made to "float" on the surface of a glass of water. Water is cohesive.

The Great Salt Lake contains high quantities of mineral solutes. Water is a good solvent.

The coastal areas of the world have a climate that is more moderate than inland areas. Water has

a temperature-stabilizing capacity.

Some springs contain high amounts of arsenic. Water is a good solvent.

Many insects, such as the water strider, are able to move across the surface of water. Water is

cohesive.

What atom forms the backbone of almost all biological molecules?

carbon

Which of the following is not a fundamental property of carbon?

Carbon atoms are most likely to form ionic bonds with one another.

The cell membrane is composed of a bilayer of ________. These molecules have regions that are polar
and nonpolar and are therefore ________.
phospholipid, mosaic

A selectively ________ membrane is one that allows some molecules to pass through but not others.
Permeable
 Although energy is ________ for polymerization, most macromolecules fold into their final three-
dimensional conformations ________.
essential statically
TMV, or ________, is a rodlike particle with a genome of ________ and a ________ consisting of
2130 copies of a single polypeptide.
Tabacco Mosaic Virus, single strand RNA

Which of these amino acids is considered to be nonpolar

Valine

Some proteins within cells contain hydrophillic amino acids and hydrophobic amino acids. What’s
the difference between a hydrophilic and a hydrophobic molecule?
hydrophobic molecules nonpolar and do not like water, hydrophilic molecules are polar and like
water bonding.
Many cellular structures are held together by non-covalent bonds and interactions. Name
the 4 given in class.
van der wals
london dispersion forces
hydrogen bonds
covalent/ ionic
glycosidic bonds

Which one of these interactions/bond is the most important for making the protein's secondary
structure?

hydrogen bonds
Which bond/interactions is the most important for the tertiary structure?

hydrophobic interactions
There was one covalent bond that was mentioned specifically giving proteins major stability in folding.
Which covalent bond is this?
di-sulfide bonds

There are many types of proteins and several were listed in class. Please give me 5 different
classes of proteins and their main function/role.
Collagen, globular, keratin, elastin, fibrous

What type of bond does a peptide bond make?

Covalent bond
Homework Questions:
● Homework 4

Which of the following would most accurately describe the state of a sarcomere if myosin were
mutated such that it had a much higher affinity for ADP but a normal affinity for Pi?

The myosin head will be engaged in a cross-bridge to the thin filament but prior to the
power stroke.

Tubulin may assemble onto one end while disassembling from the other end of the same
microtubule simultaneously in a process known as
Treadmilling

The two main types of eukaryotic microtubules are the ________ and ________ microtubules.
cytoplasmic; axonemal

________ is a drug that blocks cell division by stabilizing microtubules; as a result, it is used in
the treatment of ________.

Taxol; breast cancer

What are the 3 types of secretion discussed in class. Give a sentence or 2 describing each type.
Constitutive Secretion : After budding from the TGN, some vesicles move directly to the
cell surface and immediately fuse with the plasma membrane.

Regulated Secretion: Secretory vesicles first accumulate in the cell and fuse with the plasma
membrane only in response to specific signals (e.g. neurotransmitter release)

Polarized Secretion: In many cases, exocytosis of specific proteins is limited to a

specific surface of the cell

Which of the following is false about dynamic instability of a microtubule end?

Each end of a microtubule can undergo dynamic instability independently.
During rescue, GTP-tubulin assembles fast enough to reestablish a GTP cap.
During a growth phase, assembly of GTP-tubulin is faster than incorporated GTP is
hydrolyzed, forming a GTP-cap.
During a catastrophe phase, hydrolysis of incorporated GTP is faster than GTP-tubulin
addition, forming a GDP-cap.
All of the above are true.

The ________ is the organelle that fuses with endosomes and supplies hydrolytic enzymes
necessary for the digestion of the materials.
Lysosome
Motility may involve

shortening of a cell.

movement of the environment past a cell.

movement of a cell/organism through its

environment.
movement of components within a cell.

All of the above are correct.

Which of the following is not a function of the cytoskeleton?

passive
transport

Which of the following is the correct order of events in a crawling cell?

protrusion at the cell's leading edge, attachment of protrusion, pulling the cell forward, release
and retraction of trailing edge

During the sliding process in microtubules in cilia and flagella, the stalks of an axonemal dynein
attach to, produce force on, and detach from a(n) ________ in a cyclic manner.
B Tubule

Which of the following microtubule-interacting proteins would you target to disrupt cell division in
actively replicating tumor cells?
MCAK (a catastrophin)

What is a SNARE protein? How is it important for cells?

Snap Receptor proteins that are large protein complexes consisting of at least 24
members in yeasts.
They mediate vesicle fusion, that is, the fusion of vesicles with their target membrane
bound compartments (such as a lysosome)

How do cells maintain a low pH inside lysosomes? (Give me the name of this protein)
ATP dependent Hydrogen (proton) Pump

Microfilaments
 are composed of two helical strands of actin monomers oriented in the
same direction.

Which of the following statements is false regarding phagocytosis?

It is mediated by clathrin at the plasma

membrane.

Rho Family GTPases (Rho, Rac, Cdc42) stimulate cytoskeletal microfilament assembly for
all of the following except

nuclear envelope breakdown for mitosis.

Homework 2
The most prominent lipids in animal cell membranes are
Phospholipids.

The DNA Molecule is a _______-______ structure discovered by Watson and Crick in 1953?
Double-Helix

The primary structure of a protein

is the linear sequence of amino acids that are linked together by peptide bonds.

is simply the order of amino acids from one end of the protein to another.

is important for determining the secondary and tertiary structure of a protein.

is important both genetically and structurally.

All of these statements are true.

Each of the following is a function of membranes except

information storage.
 Active transport can be categorized and either indirect or direct active transport. What is the
difference between these two (biggest difference)? What is Indirect active transport is also called?
Is the NA+/K+ pump an example of direct or indirect active transport. Is the Na+/glucose
(symporter protein) an example of direct or indirect transport. How do you know whether these
two pumps are direct or indirect? Also Do these two pumps (Na+/K+ and Na+/glucose) work
together in the cell? Where do these cells work together (shown in class)?

Direct active transport involves the use of ATP and specific molecules travelling against
their concentration gradient using protein channels. Indirect active transport involves
similar sized molecules using those protein channels to travel across the barrier. The
sodium/Potassium pumps are direct active transport. They are direct because specific
channels were made to carry them across the barrier. Yes they do work together in the cell
body.

Which of the following molecules is involved with assisted assembly?

molecular chaperones

Final Exam
Lecture 26: Study the different types of mutagens and know their mode of actions (you don’t need to
remember the name of the mutagens seen in class).

For DNA repair, what is the first two mechanisms used by cells to correct mutations? (base excision repair
and NER). In case of severe DNA damage, what are the last resort mechanisms used to repair DNA? (error
prone = slide 33, I won’t ask questions about the details of how these two repair system work).

FROM THE FINAL GUIDE:

Lecture 26
Study the different types of mutagens and know their mode of actions (you don’t
need to remember the name of the mutagens seen in class). For DNA repair, what
are the first two mechanisms used by cells to correct mutations? (base excision
repair and NER). In case of severe DNA damage, what are the last resort mechanisms
used to repair DNA? (error prone =slide 33, I won’t ask questions about the details of
how these two repair systems work).

- DNA damage can be used by mutation causing agents. Environmental mutagens fall into
two categories: chemicals and radiation
- Mutation can also be induced by mobile genetic elements, such as found in viruses, or
transposable elements (transposons)

- Chemical mutagens alter the DNA through a variety of mechanisms

- Base analogues resemble nitrogenous bases and are incorporated into DNA
- Base modifying agents react chemically with DNA bases to alter their structures, forming
DNA adducts
- Intercalating agents insert themselves between adjacent bases, distorting DNA structure

Maltose, two glucose units

Lactose, one glucose linked to one galactose
Sucrose, one glucose linked to one fructose