Chem 6C exam 5

7/20/2015

1

- Remember! Extra 5% with clicker questions (up to 105% points!) - Attendance to discussion sections: 10%!!!! - The final exam will contain questions regarding the midterm, so if you grade in the final exam is better than the midterm, I might drop your midterm exam!!! - Potential 5 extra credit questions on the final.

- The percentages might be shifted (87-100% A, etc).

Midterm

Discussion sections THIS WEEK:

Our TA’s will go over the midterm questions.

You will be able to see your exam in front of your TA, BUT you CAN NOT take it with you.

If there is a mistake in the grading, tell your TA.

If there is still a discrepancy, follow the next steps:

– Only exams taken in pen, no whiteout or correction tape

– Send me an email with:

A cover letter indicating which problem and describe dispute

Provide full name and email

– Entire exam will be regraded

– I will email you back in the next 48 hours

1. ATTEND CLASS AND TAKE NOTES. Taking notes keeps you actively engaged in class. Comparing your notes with the text and with lecture notes we provide will help make clear which topics you grasp fully and which you don't. Lectures will cover some material not contained in the readings. 2. DO THE ASSIGNED READINGS. If you are having trouble following the lectures, read the textbook assignments before coming to class. Some material briefly covered in lecture will be more extensively described in the readings. 3. USE THE TEXTBOOK WEBSITE. There are a host of tutorials, guides, and self-quizzes available to help you learn and review the material. Some questions from self-quizzes will be used verbatim in exams!

Tips for success in class Tips for success in class

4. LEARN THE VOCABULARY. You cannot understand complex biological concepts if you are not familiar with the words that are being used. Definitions can be found in the glossary of your textbook and online. 5. ATTEND SECTIONS. Hearing and seeing material presented in a smaller group and from a different perspective can be enormously beneficial. Discussion leaders will elaborate on answers to your questions. 6. TALK TO THE INSTRUCTOR AND TAS. If you have a question or problem, visit the instructor during office hours. Put our office hours in your weekly schedule planner. We have scheduled this time to meet and talk with you, so please don’t hesitate to stop by and ask questions.

7/20/2015

2

7. WORK WITH YOUR CLASSMATES. Connect with your peers and set up informal study sessions or formal study groups. Also take advantage of the online message board for group discussions with fellow students, TAs and instructors. 8. TAKE ADVANTAGE OF CAMPUS PROFESSIONAL SERVICES: A. OASIS (HTTP://OASIS.UCSD.EDU/) The Office of Academic Support & Instructional Services gives students access to counselors who can help them develop reading and writing strategies, design better time management systems, write more effective class notes, and organize writing assignments. B. PSYCH SERVICES (HTTP://PSYCHSERVICES.UCSD.EDU/) Confidential and free counseling and psychological services related to a wide range of problems, including poor academic performance and study skills, homesickness, roommate conflicts, alcohol and other substance use and abuse, relationship difficulties, and depression. C. ACADEMIC ADVISORS. Both your college and your department have professional staff responsible for helping students in choosing appropriate plans of study and coping with any academic difficulties.

Tips for success in class

Source: http://www.wilsondailyprep.com/

Source: http://wishiwasherethefilm.tumblr.com/

Source: https://www.pinterest.com/

7/20/2015

3

The Cell Cycle: Mitosis What is the cell?

The cell is the smallest living thing that can

perform all the functions of life:

- Nutrition

- Communication

- Reproduction

Why is it important for cells to divide?

Regarding cells in a multicellular organism, they must

undergo cell division in order to:

The ability of unicellular

organisms to reproduce

Source: http://www.tutorvista.com/

1. https://www.youtube.com/watch?v=eQNxHGpK7Wc

2.

7/20/2015

4

Source: http://book.bionumbers.org/

3.

The cell cycle

- produces two genetically identical cells -

Source: http://www.slideshare.net/

Cell Division?

All steps are highly regulated to ensure precise cell

division, resulting in two identical daughter cells

Division of the cytoplasm into 2 cells (Cytokinesis)

2 Daughter cells

Figure 12.9

Division of chromosomes into 2 nuclei (Mitosis)

7/20/2015

5

Cellular organization

of the genetic material

• All the DNA in a cell constitutes the cell’s

genome

• A genome can consist of a single DNA

molecule (common in prokaryotic cells) or

a number of DNA molecules (common in

eukaryotic cells)

• DNA molecules in a cell are packaged into

chromosomes (individual DNA strands)

• Each eukaryotic chromosome constists of

one very long, linear DNA molecule

associated with proteins.

• Each chromosome contains hundred to

thousand of genes.

Source: http://www.pgpstudy.org/

A gene is a locus (or region) of DNA that encodes a functional RNA or protein product, and is the molecular unit of heredity

Every somatic cell in your body has the exact same DNA

(genome).

A. True

B. False

Clicker question 1 The total length of DNA in a typical cell is ~ 2 meters!!

This is 250,000 X greater than the diameter of the cell!

7/20/2015

6

The genetic material must be organized

somehow to fit into the nucleus!!!!

• DNA is double stranded

• It wraps around histones

to form nucleosomes,

together called chromatin

• Chromatin wraps around

itself and condensates to

form a coiled coil

chromatin bundle

• The most tightly packed

form of DNA is found in a

dividing cell


of the genetic

material

http://www.bio.miami.edu/

DNA double

helix

DNA wraps

around histones

chromatin chromatin

coiled coil

chromatin

unduplicated

chromosome

Clicker question 2

Is this cell haploid or diploid?

A) haploid

B) diploid

http://biology.westfield.ma.edu/

• Somatic cells (non-reproductive cells)

– Have two sets of chromosomes

– Humans have ____chromosomes

in somatic cells (2n=diploid)

• Gametes a.k.a. reproductive cells

– Sperm and eggs

– Have half as many chromosomes as

somatic cells

– Humans have _____chromosomes in

gametes (n=haploid)


of the genetic material

7/20/2015

7

Saladin K., Anatomy and Physiology: The Unity of Form and Function, 3rd Ed.

If chromosomes look like this

what are these then?

http://biology.westfield.ma.edu/

Figure 9.4

Centromere 0.5 m

Sister chromatids

The structure of a duplicated chromosome

Identical to

DNA is always present in the cell in the form of condensed

chromosomes.

A. True

B. False

Clicker question 3

Chromosomes

Centrosomes

(with centriole pairs) Chromatin

(duplicated)

Nucleolus Nuclear

envelope

Plasma

membrane

7/20/2015

8

INTERPHASE

G1

G2

S

(DNA synthesis)

The mitotic phase alternates with interphase in the cell cycle

Interphase

Stage What happens?

G1 “First Gap” Cell growth

S “Synthesis” Cell growth. DNA duplication.

G2 “Second Gap” Cell growth

Mitotic phase

Mitosis

Cytokinesis

Overview of Cell Division

Stage

Prophase

Prometaphase

Metaphase

Anaphase

Telophase

These overlap

INTERPHASE

G1

G2

S

(DNA synthesis)

The mitotic phase alternates with interphase in the cell cycle

INTERPHASE

G1

G2

S

(DNA synthesis)

When do chromosomes

duplicate?

7/20/2015

9

S Phase: DNA Duplication

All of the cell’s DNA must be copied in order to distribute

one genome to each daughter cell

(Replication, discussed on Wednesday)

Genome total DNA containing an organism’s complete set of genes

Bacterial genome 4.6 x 106 base pairs (E. coli)

Fruitfly genome 1.2 x 108 base pairs

Human genome 3.3 x 109 base pairs

Chromosome 1 unit of double-stranded DNA; 1 set contains the genome

Bacteria 1 circular chromosome (1 total)

Fruitfly 2 sets of 4 chromosomes (8 total)

Human 2 sets of 23 chromosomes (46 total)

Diploid cells carry 2 sets of chromosomes, maternal & paternal

Source: http://bio1100.nicerweb.com/

INTERPHASE

G1

G2

S

(DNA synthesis)

When are chromosomes

condensed?

Interphase

Stage What happens?

G1 “First Gap” Cell growth

S “Synthesis” DNA duplication

G2 “Second Gap” Cell growth G2 OF INTERPHASE

Centrosomes

(with centriole pairs) Chromatin

(duplicated)

Nucleolus Nuclear

envelope

Plasma

membrane

End of Interphase:

- DNA duplicated

- centrosomes duplicated

Figure 12.6

7/20/2015

10

INTERPHASE

G1

G2

S

(DNA synthesis)

Mitosis

Prophase

Prometaphase

Metaphase

Anaphase

Telophase

Mitotic Phase

Cytokinesis

Source: http://www.askavetquestion.com/

Source: http://tinleytime.blogspot.com/

Remember… PPMAT

G1

G2

S

Clicker question 4

There are cells that never/almost never divide such as neurons. In which part of the cell cycle you think are they ?

A) S B) G2 C) Mitotic phase D) G1

7/20/2015

11

Prophase

Early mitotic

spindle

Aster

Centromere

Chromosome, consisting

of two sister chromatids

By End of Prophase:

- Chromosomes condense, sister chromatids

are visible by microscopy

- Mitotic spindle begins to form

- Centrosomes begin to separate

Figure 12.6

Centrosome

Prophase: Condensation of Duplicated Chromosomes

Figure 12.3 - .4

50 µm

condensed

chromosomes

Prometaphase

By End of Prometaphase:

- The nuclear membrane has disintegrated

- Centrosomes at opposite ends of cell

- The ends of the mitotic spindle attach to

kinetochores on each chromatid

Figure 12.6

Metaphase

By End of Metaphase:

- Chromosomes aligned along ‘metaphase plate’

- Sister chromatids are each attached to

kinetochores from opposite pole centrosome

- Mitotic Spindle fully formed

Figure 12.6

Spindle

Metaphase

plate

Centrosome at

one spindle pole

7/20/2015

12

Anaphase

Daughter

chromosomes Figure 12.6

By End of Anaphase:

- Sister chromatids separate into 2 chromosomes: separase

- Kinetochore microtubules shorten

- Non-kinetochore microtubules lengthen to elongate cell

Telophase

By End of Telophase:

- Two nuclei begin to form

- Chromosomes become less condensed

- End of mitosis

- Cytokinesis completes cell division by

pinching cells in two via formation of a

cleavage furrow (animals) or a cell wall

(plants)

Figure 12.6

Cleavage

furrow

Nuclear

envelope

forming

Nucleolus

forming

Cleavage furrow

• Nonkinetochore microtubules from opposite poles overlap and push

against each other, elongating the cell

• In telophase, genetically identical daughter nuclei form at opposite

ends of the cell

• Cytokinesis begins during anaphase or telophase and the spindle

eventually disassembles

Cytokinesis

- division of the cytosol into two cells -

emerging cleavage furrow

cleavage furrow

Cytokinesis

- division of the cytosol into two cells -

Cleavage furrow separates

cytoplasm of animal cells by

actinomyosin ring

constriction

Cell plate separates

cytoplasm of plant cells by

localized membrane addition

plant cells do not

have centrioles

7/20/2015

13

Don’t Be Confused by the Collection of C-words

Chromatin

Chromosome

Chromatids

Centromeres

Centrosomes

Cytokinesis

Video mitosis: https://www.youtube.com/watch?v=C6hn3sA0ip0

Remember! Prokaryotic chromosome… so different from eukaryots! Also, no

microtubules!! How can bacteria divide then?

Figure 9.12-1

1

Origin of replication

Two copies of origin

Bacterial chromosome

Plasma membrane

Cell wall

E. coli cell

Chromosome replication begins.

Binary Fission in Bacteria

Figure 9.12-2

1




Plasma membrane

Cell wall

E. coli cell

Origin Origin


2 One copy of the origin is now at each end of the cell.

7/20/2015

14

Figure 9.12-3

1




Plasma membrane

Cell wall

E. coli cell

Origin Origin


2

3

One copy of the origin is now at each end of the cell.

Replication finishes.

Figure 9.12-4

1




Plasma membrane

Cell wall

E. coli cell

Origin Origin


2

3

4

One copy of the origin is now at each end of the cell.

Replication finishes.

Two daughter cells result.

Figure 9.13

Chromosomes

Intact nuclear envelope

Microtubules

Kinetochore microtubule

Intact nuclear envelope

(a) Dinoflagellates

(b) Diatoms and some yeasts

But biology is not black or white… The cell cycle must be tightly regulated…

7/20/2015

15

Source: http://book.bionumbers.org/ Source: http://rise.duke.edu/

Cancer: “just” uncontrolled cell division

A molecular control system regulates the eukaryotic cell cycle

Where is this molecular control system?

Figure 9.14

G1 nucleus immediately entered S phase and DNA was synthesized.

Experiment

Experiment 1 Experiment 2

Results

S

S S

M G1

M M

G1

G1 nucleus began mitosis without chromosome duplication.

Conclusion Molecules present in the cytoplasm control the progression to S and M phases.

7/20/2015

16

A checkpoint in the cell cycle is a control point where stop and go-ahead signals can regulate the cycle.

G1 checkpoint

G1

G2

G2 checkpoint

M

S

Control system

M checkpoint

• The cell cycle

control system is

regulated by both

internal and

external controls

• The clock has

specific

checkpoints where

the cell cycle stops

until a go-ahead

signal is received

• For many cells, the

G1 checkpoint

seems to be the

most important

Figure 9.16a

G1

G1 checkpoint

Without go-ahead signal, cell enters G0.

G0

With go-ahead signal, cell continues cell cycle.

(a) G1 checkpoint

G1

Figure 9.16b

M checkpoint

M

G1

G2

Prometaphase

Without full chromosome attachment, stop signal is received.

(b) M checkpoint

M

G1

G2

G2

checkpoint

Metaphase

Anaphase

With full chromosome attachment, go-ahead signal is received.

Clicker question 5 – Case study

You are a researcher, and you think you’ve found a new mutation in a

gene that causes cancer. You notice that the cells that have this

mutation replicate their DNA when normal cells do not. You think that

these cells have a mutant protein that cannot act at a checkpoint.

Which checkpoint is affected?

A) G1 checkpoint

B) M checkpoint

C) G2 checkpoint

D) Not sure

INTERPHASE

G1

G2

S (DNA duplication)

7/20/2015

17

Factors that control cell cycle: External (to the cell):

- Biological factors: Growth factors (example of PDGF: platelet-derived growth factor) - Physical factors: density-dependent inhibition, anchorage-dependent inhibition.

Internal

Figure 5.20-1

EXTRACELLULAR FLUID Plasma membrane

Reception

Receptor

Signaling molecule

CYTOPLASM

Cell signaling: three stages

Figure 5.20-2

EXTRACELLULAR FLUID

CYTOPLASM

Plasma membrane

Reception Transduction

Relay molecules

Receptor

Signaling molecule

Cell signaling: three stages Figure 5.20-3

EXTRACELLULAR FLUID

CYTOPLASM

Plasma membrane

Response Reception Transduction

Relay molecules

Activation

Receptor

Signaling molecule

Cell signaling: three stages

7/20/2015

18

Figure 9.17-1

1 A sample of human connective tissue is cut up into small pieces.

Petri dish

Scalpels

Figure 9.17-2


2 Enzymes digest the extracellular matrix, resulting in a suspension of free fibroblasts.

Petri dish

Scalpels

Figure 9.17-3


2

3

Enzymes digest the extracellular matrix, resulting in a suspension of free fibroblasts.

Cells are transferred to culture vessels.

Petri dish

Scalpels

4 PDGF is added to half the vessels.

Figure 9.17-4


2

3

4

Enzymes digest the extracellular matrix, resulting in a suspension of free fibroblasts.

Cells are transferred to culture vessels. PDGF is added to

half the vessels.

Without PDGF With PDGF Cultured fibroblasts (SEM) 10 m

Petri dish

Scalpels

7/20/2015

19

Figure 9.18

Anchorage dependence: cells require a surface for division

20 m

Density-dependent inhibition: cells divide to fill a gap and then stop

Density-dependent inhibition: cells form a single layer

20 m

(a) Normal mammalian cells (b) Cancer cells

Controlling the cell cycle clock

• Two types of regulatory proteins

are involved in cell cycle control:

cyclins and cyclin-dependent

kinases (Cdks)

• Cdk activity fluctuates during the

cell cycle because it is

controlled by cyclins

• MPF (maturation-promoting

factor) is a cyclinB - Cdk1

complex that triggers a cell’s

passage past the G2 checkpoint

into the M phase by

phosphorylating many proteins

which are needed during mitosis

MPF

Cdk 1 CyclinB

Active!

P

Cdk1

Degraded cyclin B

Cyclin B is degraded

MPF

G2 checkpoint

Cdk1

Cyclin B P

• Cancer cells

– Do not respond normally to the body’s control mechanisms

– May not need growth factors to grow and divide

• May make their own growth factors

• May convey a growth factor’s signal without

the presence of the growth factor

• May have an abnormal cell cycle control system

Loss of cell cycle controls in cancer

cells

http://leonardonoto.com/

7/20/2015

20

The growth and metastasis of

a malignant breast tumor • A normal cell

– Converted to a cancerous cell

– Process called transformation

• Cancer cells

– Form tumors

– Masses of abnormal cells within otherwise normal tissue

• If abnormal cells remain at the original site

– The lump is called a benign tumor

• Malignant tumors

– Can metastasize: invading surrounding

tissues

• Exporting cancer cells to other

parts of the body

• May form secondary tumors

1) 2)

3) 4)

Most cancers that are lethal because of metastasis

Documents

Chem 6C exam 5