Study Guide for Lectures 9-16 (Chapters 9, 11, 12 and 14)

Lecture 9 and 10 Cell Signaling (Chapter 9)

1. Cell communication is composed of 4 key components. Fill in the table describing the
role of each component in the signaling process.
Signaling cell Signaling molecule Receptor protein Responding cell.
sends signaling aka ligand, ligand bonds Takes in ligand into respond is affected by receptor and
molecule to receptor to ligand binding site cell, conforms, polar area signaling molecule
on responding cell on receptor, causing intra- binds to polar ligand outside
cellular signaling, can cause cell, intracellular receptor
conformational change in binds to small nonpolar ligand
receptor
2. When a receptor receives a signaling molecule a series of events will occur to invoke and
then terminate the response. Describe in general what happens at each event in the
table below.
Receptor activation Signal Transduction Response Termination
proteins may need to bind to diff. parts of receptor can bind end of pathway
something to become active, to diff. molecules and diff. signaling molecules elicit
transduction proteins specific responses in certain
cells
blocking signalling molecule, stopping
transcription in nucleus signaling cascade by phosphorylation

3. Ligand-receptor interactions can take place on the cell-surface or inside the cell.
Compare and contrast these 2 types of interactions.

Cell-surface receptors Intracellular receptors

Is the signaling hydrophilic because it can not pass hydrophobic because it can pass through
phospholipid bilayer to bind with receptor
molecule generally through nonpolar plasma membrane
without receptor
hydrophobic or
hydrophilic? Explain
What types of amino polar , polar ligand in aqueous environment
nonpolar, nonpolar ligand
acids will be on the
ligand binding site on
the receptor? Explain

4. Protein phosphorylation often results in activation of a protein. Fill in the table below.
Which amino acids are usually serine, tyrosine, threonine

phosphorylated on a target
(free OH groups)
protein?
Which enzymes phosphorylate kinases

proteins?
Which enzymes phosphotase
dephosphorylate proteins?
Give some effects of kinase taking phosphate group from ATP creating ADP
phosphorylation that will
can provide a new site for proteins to bind to, can lead to degradation of certain
activate a protein. proteins.
(activation and binding especially)
5. Name and describe each of the key stages of signaling via a G protein coupled receptor.
Step 1: ligand binds to extracellular portion of receptor, intracellular portion of receptor changes shape to bind to G protein.
alpha binds to GTP instead of GDP, alpha detaches from beta and gamma so that alpha can move through plasma membrane and
activate target protein, causing a response
Step 2: G protein signal transduction. Activated adenylyl cyclase converts ATP->cAMP, this binds to and activates protein kinase A,
PKA phosphorylates proteins and causes response

6. List and describe the key ways in which a signal can be amplified from a response
initiated at a G protein coupled receptor.
ligand binds to and activates receptor, receptor can activate multiple alpha subunits of multiple G proteins. Many G proteins can activate
many adenylyl cyclases, convert ATP to cAMP, lots of cAMP will activate lots of PKA's which will phosphorylate lots of protein targets

7. List and describe the key ways in which a signal can be terminated from a response
initiated at a G protein coupled receptor.
Can reduce amount of ligand, hydrolyze GTP into GDP which will inactivate the alpha subunit and allow it to interact with B & Y,
cAMP can be converted to AMP which will not allow PKA to be activated, and target protein can be dephosphorylated by phosphotase
which will inactivate it.
Multiple or all of these have to occur to terminate

8. List and describe the key steps to activate a receptor kinase.

2 unconnected subunits, signaling molecule will cause it to conform and move together, dimerization turns it into a kinase, subunits
phosphorylate each other by taking phosphate from ATP and have phosphate groups on intracellular part of receptor, this activates the
receptor and creates binding sites for other proteins inside the cell that are part of the cascade.

9. What is Ras and when is it active and inactive?

Ras is a G protein or GTPase, GDP is exchanged for GTP to activate Ras which triggers a cascade. This activates MAP kinase,
phosphorylates
another kinase and activates it, this 2nd kinase phosphorylates a 3rd kinase and activates it, then goes to nucleus to change gene expression.
Ras is only active when it is bound to GTP and inactive when bound to GDP

10. How is amplification achieved in the MAP kinase pathway?

One GTP will activate multiple kinases then each kinase will phosphorylate another kinase
 11. The MAP kinase pathway ends in the nucleus. What is the final destination (types of
proteins affected) of the signals in this pathway and what general changes do they cause
in the nucleus?
transcription factors cause genes to change and do things

transcription factors (proteins) in the nucleus to induce cell division, proliferation, or growth

12. Name and explain several ways in which the MAP kinase pathway can be controlled
(inhibited)? is this asking how is it terminated?
Reduction/removal of signal
convert Ras GTP to Ras GDP
phosphotases remove phosphates from active receptor and downstream kinases

13. Give several general examples of how signaling pathways e.g. over production of
receptors, can be perturbed and result in uncontrolled cell proliferation leading to
cancer.
mutations in receptors and signaling pathways can cause cancer
overproduction of signaling molecules, inability to inactivate signaling proteins (Ras) and over production of receptors can all lead to cancer
too many signals, inability to turn off or activate, over production of receptors cause too many signals to be taken in

Lecture 11 Chromosomes, Mitosis and the cell cycle (Chapter 11)

1. Explain the difference between haploid and diploid cells.
Diploid- 1 complete maternal set and 1 complete paternal set, haploid- 1 complete set of each type of
chromosome

2. Why must the chromosomes be replicated before cell division?

So that 2 daughter cells receive 2 sets of every chromosome (1 single strand chromosome into 1 x shaped
chromosome when replicated.)
3. In diploid organisms the inherited paternal and maternal chromosomes, for each type of
chromosome, are homologous not identical. Explain why.
types of genes and order of genes are same but nucleotide bases are different. This is because one
chromosome has the characteristics from one parent and the other from the other parent for the same
phenotype/thing that its coding for
4. During prophase I, for one particular type of chromosome e.g. chromosome 1..
i) How many chromosomes are present?
2
ii) How many chromatids are present?

4
 iii) How many molecules of double-stranded DNA are present?

5. What is mitosis, what type of cells undergo mitosis and why?

Mitosis is the process in cell division by which the nucleus of the cell divides in multiple phases, creating two
identical daughter cells. Mitosis happens in all eukaryotic cells (plants, animals, and fungi). It is the process of cell
renewal and growth in a plant, animal or fungus.

somatic cells

6. Fill in the table below for the 4 stages of the cell cycle (including exit into G0).
Stage Events/Purpose
G1 Cells grow larger and copy organelles, see if it's big enough before division

G0 cell cycle arrest If a checkpoint finds an error

S-phase DNA replication

G2 Growth and preparation for mitosis, see's if it has enough organelles

Mitosis
single cell divides into 2 identical daughter cells

7. In general, what are cyclin-dependent-kinases (CDKs), what makes them active, and
what do they do when active?
Cyclin binds to and phosphorylates kinases to make CDK, CDK's regulate the cell cycle and push cycle forward.

CDK's become active when binded to cyclins, so these cyclin-CDK complexes can phosphorylate target proteins

CDK's are always present within the cell but are only active when bound to the appropriate cyclin.

8. Fill in the table for the following cyclins.

Cyclin Purpose/Role?
D and E In G1, these rise and activate CDK's, which allows the cell to enter S phase
activate transcription factors and activate DNA polymerase for replication
A In S phase, these activate CDK's that inhibit DNA synthesis enzymes once DNA replication
is complete so that the same DNA sequence isn't replicated (too much DNA could cause cancer or cell death
B In G2, these activate CDK's that activate enzymes for mitosis, like phosphorylating structural proteins in nucleus
that break down nuclear envelope in prometaphase, and phosphorylates proteins that regulate the assembly
of tubulin into microtubules, promoting formation of mitotic spindle
Lecture 12 Cancer, meiosis and meiosis v mitosis (Chapter 11)
1. What is a tumor and what is the cause?
uncontrolled cell division, caused by inappropriate activation of certain cell cycle stages and checkpoint failures
metasteses move to other tissues (malignant), cyclins, CDKs, signaling, RAS,any proteins that move cycle forward
can mutate (over activity)
2. What are tumor suppressors?
checkpoint failures can cause underactivity
tumor suppressors halt cell cycle progression if cell doesn't pass checkpoint standards.
P53 affects G1/S transition by making sure DNA isn't damaged and stops it from going into S phase

3. What happens when a tumor suppressor acquires a loss-of-function mutation?

uncontrolled cell division

4. Fill in the table below for P53.

Tumor Which What state or What happens to the cell
suppressor/proto- stage of modifications cycle when it is activated,
oncogene the cell must occur to and what decision must
cycle activate it? the cell make?
does it
act in?
DNA damage activates
P53 tumor suppressor inhibits cyclins, decides if it should fix it or kill itself
G1/S protein kinases that
transition phosphorylate P53 (apoptosis)

must be in quaternary
structure plays a roll in cell cycle arrrest

5. What is a proto-oncogene, what is an oncogene and how are the two related?

protooncogenes promote normal cell growth and division, oncogenes promote uncontrolled cell growth and
division (proliferation)

6. Why do you need more than one inactive tumor suppressor and active oncogene to
cause cancer?
You need multiple mutations because just one mutation can be fixed later in the cell cycle

7. What is the difference between somatic cells and germ-cells?

germ cells are haploid and produce gametes, somatic make body cells that make 2 identical cells

8. What type of cells divide by meiosis and why?

germ cells

greater genetic variation

meiosis 1 is reductional division because chromosomes go 46 to 23
meiosis 2 is equational division because end of meiois 1 = haploid, after meiosis 2 = haploid also (1 complete set)

9. Compare and contrast meiosis and mitosis stating all of the key events that occur at
each stage.
Stage Meiosis Mitosis
Prophase I
-Centrosomes move to side of cells
-DNA is already replicated crossing over
-Pairing of chromosomes and exchange
genetic material (bivalent) (only in M1)
-Chromosomes are thin threads
-Homologous chromosomes continue to
condense and undergo synapsis
-like genes line up from nonsister chromatids
-Chiasma- breaking and joining of these chromatids
-Result: 1st stage of meiosis contributes to genetic
variation

Prometaphase I -Spindles attach to kinetochores on chromosome

-nuclear membrane disappears

Metaphase I -chromosomes (bivalents) are not in single file line

in middle but aligned with each other and oriented
randomly

random alignment leads to genetic variation

Anaphase I chiasmata breaks

-homologous chromosomes separate but sister
chromatids do not separate
-pulling whole chromosomes apart to sides of cell
-daughter cells are haploid

Telophase I and -daughter cells are ready to move into prophase II

cytokinesis
nuclear envolopes may reform or cell may
quickly start Meiosis II

Prophase II Prophase
tangled chromatin inside nuclear
- No DNA replication before
envelope condense into chromosomes

nuclear envelope starts to break down

Prometaphase II Prometaphase
-Now spindle fibers from each pole attach to each
side of centromere chromosomes are attached to spindles
chromosomes align in center
Metaphase II -align in center Metaphase so it splits evenly

Anaphase II Anaphase
centromeres split from spindle fibers pulling apart proteins that hold sister chromatids
get broken and split part to ends of cell

Telophase II Telophase
A nuclear membrane forms around each haploid Each daughter cell will have 2
set of chromosomes sets of chromosomes

cells divide forming into haploid gametes, 4 sperm

Cytokinesis or 1 egg cell (3 eggs die) Cytokinesis polymerization at one end

4 haploid daughter cells are formed from original

diploid cell when it entered meiois

Number of daughter 4 2

cells produced
Are daughter cells no
identical to each yes

other and to the

parental cells?
10. Meiosis allows for genetic variation. Fill in the table below.
Process that results in Stage at which this process How does the stage in
genetic variation occurs in meiosis or fertilization
meiosis/fertilization allow for genetic
variation?
Crossing over prophase 1 creates recombinant chromosomes

Independent assortment metaphase 1 could get copies of only paternal or only

maternal cells or a mixture of both
separating sister chromatids to get a lot of
combinations
Final gametes fertilization one chromosome from one gamete from
father and one from mother, combination in
offspring

11. a What is non-disjunction and in what stage of cell division does it typically
occur?
Incorrect alignment of chromosomes during anaphase of meiosis 1 or 2

b What problems in (a) can cause non-disjunction?

can end up with daughter with too many or no chromosomes

c With respect to chromosomal numbers how do daughter cells differ from normal if
non-disjunction has occurred?

d Non-disjunction can occur in meiosis as well as mitosis. For a germ cell undergoing
meiosis (to produce 4 gametes), what proportion of the gametes will contain the
incorrect number of chromosomes if non-disjunction occurs in meiosis I?

in meiosis 1 it will affect all daughter cells

in meiosis 2 it will affect half of them
 e Non-disjunction can occur in meiosis as well as mitosis. For a germ cell undergoing
meiosis (to produce 4 gametes), what proportion of the gametes will contain the
incorrect number of chromosomes if non-disjunction occurs in meiosis II?

Lecture 13 DNA replication (Chapter 12)

1. What is the semi-conservative theory of DNA replication?
initial strands of DNA are template of synthesis of daughter DNA

2. In what direction is DNA replicated?

5' to 3'

3. In what direction is the DNA template read to copy and synthesize the new DNA strand?
3' to 5'

4. In order to copy both DNA strands from a parental duplex, a leading strand and lagging
strand is produced. What are the key differences between the ways each is produced and
why is the mechanism different?
leading strand is continuous DNA synthesis, lagging is fragmented
both need RNA primer to start

5. List the key enzymes required for DNA replication, their function and the order in which
they act.

RNA primase
DNA polymerase- synthesizes new strand
Ligase- ties fragments together

6. For linear chromosomes, why is there a problem with completing the very end of the
lagging strand and how is this problem resolved by the inclusion of a telomere sequence?

leading strand finishes replication before lagging strand

telomeres adds DNA that are not coded for, just prevent any important DNA from getting cut off

telomeres are the plastic part of shoe laces

 7. In which type of cells is telomerase activity high, and why is it high?

telomerase extends telomeres, its high in stem and germ cells

8. Why is telomerase reactivation often detected in cancerous cells?

when telomeres get too short it leads to aging
if you keep extending telomeres then theyll bipass this cell death and continue to proliferate

Lecture 14 DNA manipulation (Chapter 12)

1. The Polymerase Chain Reaction (PCR) consists of 3 key repeating steps. List these steps
and briefly explain what happens.
denaturing, annealing, extension

double strand is heated up so it can be divided in to 2 strands

cooled so RNA primers can be DNA polymerase synthesises new DNA strand
2. What are the 3 requirements for primers used in PCR?
1. primers used in PCR are DNA primers (replication uses RNA0
2. COmplementary to bases
3. Antiparallel
3. Compare and contrast DNA replication in the cell with PCR. What are the similarities and
differences?
both cells use DNA polymerase to synthesize new DNA strand
PCR is similar to leading strand synthesis because it is continuous and is replicated 5' to 3'

replication uses RNA primers, PCR uses DNA primers

Lecture 15 Small scale mutations (Chapter 14)

1. What is a mutation?
any change in the nucleotide sequence that can be heritable

2. What causes mutations?

spontaneous but can be caused by environment (UV or chemicals), viruses, or passed down to offspring

cellular conditions like if theres a build up of oxygen inside the cell

3. Certain mutations cause cancer. These mutations can arise in either somatic or
germ-cells, but only one could be hereditary. Which one could be passed down onto
offspring and why?

germ cells because these are passed to off spring

 4. What is a point mutation?
a mutation in one specific nucleotide

5. Fill in the table for the 3 types of point mutations.

Type of point mutation Does the point mutation If the amino acid has changed will
in the codon change the it impact the function of the
amino acid? protein? Explain how.
Silent (synonymous) no
missense yes changes the amino acid
(nonsynonymous)
nonsense turns to stop codon
yes

6. What is the mRNA reading frame and what dictates the frame?
start codon AUG - methionine

7. Mutations can also be in the form of an insertion (of one or more bases), a deletion
(of one or more bases). What does this do to the reading frame and the protein
sequence that is translated?
if youre adding or removing a base, it could change the reading frame downstream, could change how the
protein is folded and loses function

8. Mistakes can be made in the DNA sequence during DNA replication, the mRNA
sequence during transcription or the protein sequence during translation. Which
one will likely have the most dramatic effect on an organism and why?
DNA because its further upstream in the central dogma
DNA is read multiple times not just one time like RNA

Lecture 16 DNA Repair (Chapter 14)

1. DNA polymerase has a proofreading function as well as its DNA synthesis function. How
does the proofreading function work?
if DNA polymerase notices an error in nucleotide, removes it in 3' to 5'

2. Which enzyme repairs the phosphodiester backbone?

Ligase
3. Describe the key steps of DNA damage mismatch repair.

4. Describe the key steps of DNA damage excision repair.

5. Describe the key steps of nucleotide excision repair.

6. What effect, if any, will a loss of function mutation in a DNA repair enzyme have on….
i) the rate at which mutations accumulate in a given segment of DNA?
no influence on the rate you get them because they are spontaneous

faster from mutagens and carcinagens (outside influences)

ii) the number of mutations found in a given segment of DNA?

get more mutations

iii) the DNA replication process?

once you have a mutation itll keep replicating so it won't affect the replication process
because DNA polymerase doesn't know it's not supposed to be there