A Tour of the Cell - Useful Advice€¦ · Chapter 6 A Tour of the Cell . Overview: The Fundamental Units of Life • All organisms are made of cells • The cell is the simplest

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

PowerPoint® Lecture Presentations for

Biology Eighth Edition

Neil Campbell and Jane Reece

Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp

Chapter 6

A Tour of the Cell

Overview: The Fundamental Units of Life

• All organisms are made of cells

• The cell is the simplest collection of matter that can live

• Cell structure is correlated to cellular function

• All cells are related by their descent from earlier cells


PresenterPresentation NotesFor the Discovery Video Cells, go to Animation and Video Files.

Fig. 6-1

PresenterPresentation NotesFigure 6.1 How do cellular components cooperate to help the cell function?

Concept 6.1: To study cells, biologists use microscopes and the tools of biochemistry • Though usually too small to be seen by the

unaided eye, cells can be complex


5

Metric Review

• 1 meter (m) = ~3 feet

• 1 meter (m) = 1000 millimeter (mm)

• 1 millimeter (mm) = 1000 micrometer (µm) (smallest size distinguished by naked eye)

• 1 micrometer (µm) = 1000 nanometer (nm) (only seen with light microscope)

• 1 mm poppy seed = (1000 µm/mm) = 1000 µm

met

ers

1 mm

1 µm

1 nm

10-3

10-4

10-5

10-6

10-7

10-8

10-9

Cells like ours

Bacteria

Viruses

Proteins

Atoms

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Fig. 6-2 10 m

1 m

0.1 m

1 cm

1 mm

100 µm

10 µm

1 µm

100 nm

10 nm

1 nm

0.1 nm Atoms

Small molecules

Lipids

Proteins

Ribosomes

Viruses Smallest bacteria

Mitochondrion

Nucleus Most bacteria

Most plant and animal cells

Frog egg

Chicken egg

Length of some nerve and muscle cells

Human height

Una

ided

eye

Ligh

t mic

rosc

ope

Elec

tron

mic

rosc

ope

PresenterPresentation NotesFigure 6.2 The size range of cells

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Fig. 6-3ab

(a) Brightfield (unstained specimen)

(b) Brightfield (stained specimen)

TECHNIQUE RESULTS

50 µm

PresenterPresentation NotesFigure 6.3 Light microscopy

Fig. 6-3cd

(c) Phase-contrast

(d) Differential-interference- contrast (Nomarski)

TECHNIQUE RESULTS


Fig. 6-3e

(e) Fluorescence

TECHNIQUE RESULTS

50 µm


Fig. 6-3f

(f) Confocal

TECHNIQUE RESULTS

50 µm


Pictures of Cells

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Fig. 6-4

(a) Scanning electron microscopy (SEM)

TECHNIQUE RESULTS

(b) Transmission electron microscopy (TEM)

Cilia

Longitudinal section of cilium

Cross section of cilium

1 µm

1 µm

PresenterPresentation NotesFigure 6.4 Electron microscopy

Cell Fractionation

• Cell fractionation takes cells apart and separates the major organelles from one another

• Ultracentrifuges fractionate cells into their component parts

• Cell fractionation enables scientists to determine the functions of organelles

• Biochemistry and cytology help correlate cell function with structure


16

Part I - Mysterious Illness • Well, Becky thought, being a dorm counselor for

freshmen was not going to be that bad. She got a free room for the year and the food was plentiful - free steaks last week at an outdoor BBQ followed by a hay ride in a horse-drawn wagon in their welcome celebration.

• But, then again, it wasn’t perfect: she had ended up covered in bug bites; some of the students got sick from eating steak that was burned on the outside and raw in the middle; the horses had mucked up the courtyard; and pigeons had roosted on the dorm roof.

• At least tonight the students were finally settling in and quieting down, she mused.

17

Part I - Mysterious Illness • Well, Becky thought, being a dorm counselor for

freshmen was not going to be that bad. She got a free room for the year and the food was plentiful - free steaks last week at an outdoor BBQ followed by a hay ride in a horse-drawn wagon in their welcome celebration.

• But, then again, it wasn’t perfect: she had ended up covered in bug bites; some of the students got sick from eating steak that was burned on the outside and raw in the middle; the horses had mucked up the courtyard; and pigeons had roosted on the dorm roof.

• At least tonight the students were finally settling in and quieting down, she mused.

18

Part I, continued…

• The quiet was shattered a few minutes later when one of the other counselors, Ann, yelled through her door:

• “Becky, we’ve got a problem. One of the students found a homeless kitten, and the girl has been keeping her in her room. I only found out because the girl, Ellie, just came to my room complaining of being sick. I felt sick too when I saw the mess that kitten made. I thought cats were born housebroken, but I guess not.”

• “Anyway, now I think Ellie might really be sick,” Ann continued. “She’s feverish and says she’s going to throw up.”

19

Becky’s Task

• The Health Center will be using the differences between organisms to diagnose and treat Ellie.

• In the next 2 minutes, list the clues in the story that help you identify how Ellie could have contracted a disease with flu-like symptoms. Come up with possible suspects (organisms) that could cause her to be sick.

20

Your Task

• Becky did an Internet search and found 5 possible suspects that could be causing Ellie’s illness.

• During this class session we will investigate the differences between them.

Concept 6.2: Eukaryotic cells have internal membranes that compartmentalize their functions

• The basic structural and functional unit of every organism is one of two types of cells: prokaryotic or eukaryotic

• Only organisms of the domains Bacteria and Archaea consist of prokaryotic cells

• Protists, fungi, animals, and plants all consist of eukaryotic cells


Comparing Prokaryotic and Eukaryotic Cells

• Basic features of all cells:

– Plasma membrane

– Semifluid substance called cytosol

– Chromosomes (carry genes)

– Ribosomes (make proteins)


23

Prokaryotes • Unicellular

• Reproduce asexually

• Composition

– Protected interior (cytoplasm) that contains genetic material (one circle of DNA) as well as complexes of protein enzymes to carry out necessary functions of gathering energy, manufacturing proteins (ribosomes), etc.

24

Prokaryotes

• Size

– 0.2-10 micrometer (µm)

• Composition

– Phospholipid membrane, many contain cell wall composed of peptidoglycan (positive for chemical Gram stain), those with little or no peptidoglycan called Gram negative (like Coxiella).

• Prokaryotic cells are characterized by having

– No nucleus

– DNA in an unbound region called the nucleoid

– No membrane-bound organelles

– Cytoplasm bound by the plasma membrane


Fig. 6-6

Fimbriae

Nucleoid

Ribosomes

Plasma membrane

Cell wall

Capsule

Flagella

Bacterial chromosome

(a) A typical rod-shaped bacterium

(b) A thin section through the bacterium Bacillus coagulans (TEM)

0.5 µm

PresenterPresentation NotesFigure 6.6 A prokaryotic cell

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Cancer Below is a picture of two human cancer cells sitting next to each other right before they're about to divide into four cells. They're derived from the now famous "HeLa" line of cancer cells, which were taken from Henrietta Lacks in 1951 and used for medical research without her permission. "Understanding how cells divide is critical to understanding how cancerous cells multiply and take over," according to Dr. Andrews.

A: The specific types of lipids present in the outer plasma membrane.

B: The type of molecule used as its genetic information.

C: Whether the genetic information is enclosed in a protective layer of phospholipid membrane bilayer.

D: Whether the organism is harmful to the cell.

Answer: C

PQ1: To distinguish between prokaryotes and eukaryotes, we need to consider:

A: A drug that prevents duplication of long strands of DNA

B: A drug that tangles up DNA circles and prevents their duplication.

C: A filtration system that rids the body of organisms under 0.5µm in size.

D: A drug that prevents phospholipids from being deposited into new cell membranes.

E: A drug that prevents mitochondria from functioning.

Answer: B

PQ4: You have an infection caused by a prokaryotic pathogen. Which of the following would make a good choice for killing off the prokaryote without harming your cells?

31

Becky’s Internet Search Results – List of Suspects

Suspect 1: Coxiella burnetii causes Q-fever. Coxiella are often found in

livestock and are excreted in milk, urine, and feces. Infection

occurs 2-3 weeks after inhalation of barnyard dust. They are 0.3-0.5 µm gram-

negative bacterium (prokaryotes) that must invade

and reside inside human cells to cause infection.

1µm

32

• Initial Identification: The Health Center collected blood samples from Ellie and observed her cells under a microscope. They identified foreign structures with DNA and outer membranes. The cells were gram negative and about 1/10 the size of her cells.

• “Ah, ha!” said Becky. “That matches one of my suspects. I knew those were a health hazard. I just need to re-check the size thing. This internet chart compares our cells to viruses and stuff.”

Ellie’s Diagnosis

33

A: Yes

B: No

Answer: B

met

ers

1 mm

1 µm

1 nm

10-3

10-4

10-5

10-6

10-7

10-8

10-9

Cells like ours

Bacteria

Viruses

Proteins

Atoms

CQ2: “Wait a minute!” Ann said. “The doctor said the blobs in Ellie’s blood were 1/10th the

size of her cells. Could they be Coxiella?”

34

A: Amoxicillin, Penicillin, and other ß-lactams

– Blocks the enzyme that normally creates links in peptidoglycan molecules.

B: Streptomycin

– Blocks prokaryotic ribosomes.

C: Ciprofloxacin hydrochloride (Cipro) – Blocks bacterial DNA gyrase enzyme needed to counteract

excessive twisting of DNA that occurs when circles of DNA are unwound to be copied into DNA or RNA.

– Answer: A

CQ1: “That’s great,” Becky said. “My Mom sent me 3 different antibiotics to kill bacteria.”

Given the description of Ellie’s test results, which antibiotic will definitely NOT work:

35

Part II: Microscope Analysis

Becky and Ann talked together outside the student’s room at the student health center the next morning.

“You’re right!” Becky exclaimed after viewing photographs of Ellie’s blood up close. “I wish I hadn’t started taking the

antibiotics. The little crescent shaped structures that I thought were the bacteria may not be. When you zoom in on them,

they show up clearly in the electron micrograph on the right. They aren’t too big to be bacteria, but they aren’t too small to

be mitochondria or some kind of protozoan parasite.”

“Wait a minute,” Ann replied. “The things on the right are the pathogens? Look at their insides, they can’t be bacteria.”

“Why not?” Becky asked.

36

Part II, Continued

1µm

37

A: Cytoplasm B: DNA C: Outer phospholipid membrane D: Ribosomes E: Membrane-bound organelles

CQ3: “Well,” Becky admitted, “there should be differences between Ellie’s cells and the little blobs they saw. Otherwise, it might mean one of my other suspects is the cause. These are some of the structures normally found in all cells.”

“No,” Ann answered, “one isn’t.”

Which structure is NOT found in all cells?

38

Eukaryotes • Uni- or multicellular.

• Reproduce asexually &

sexually.

• Composition:

– Genetic material (long linear strands of DNA chromosomes) especially isolated and enclosed in membrane (nucleus)

– Some have cell walls (plants have cellulose, fungi ß-glucan)

39

Eukaryotes

Size 10-100 (µm)Composition: Phospholipid membrane outside, as well as inside

Interior membranes separate functions such as gathering and transforming cellular energy and

manufacturing macromolecules.

40

Eukaryotic Organelles

Animal Cell Plant Cell

41

Eukaryotic Organelles

Mitochondrion

Chloroplast

Nucleus Endoplasmic reticulum

Golgi

• Eukaryotic cells are characterized by having

– DNA in a nucleus that is bounded by a membranous nuclear envelope

– Membrane-bound organelles

– Cytoplasm in the region between the plasma membrane and nucleus

• Eukaryotic cells are generally much larger than prokaryotic cells


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47


Suspect 3: Toxoplasma gondii

• Usually no symptoms, but can cause flu-like

complaints.

• Sexual life cycle occurs in cats, so infection can follow

contact with cat feces.

PresenterPresentation NotesSo, it’s less common, but you can get Toxo from your cat, under certain circumstances. Cats become infected by eating animals that have tissue cysts, mostly small rodents and birds. Cats (domestic and wild) are the only animals in which Toxo multiplies sexually, and the resulting cyst is excreted in cat feces. Here you can see a fecal cyst that contains 4 infective parasites. But this cyst is at least 3 days old. When cysts are first excreted, they are non-viable. They have to incubate in the environment for a few days before they become infective. So if you change your litterbox every 2 days, even if your cat is infected, you’re safe. But if your cat goes outside and you don’t keep the box clean, you can get it that way. But even if you don’t have a cat you can be infected with oocysts from soil and water that cats have defecated in. Even on produce that has been rinsed with contaminated water or grown in contaminated soil. In rare cases, the parasite has been transmitted via blood transfusion. More commonly, the parasite is passed during an organ transplant. Finally, back to the video clip. Toxo can be transmitted across the placenta from a mother to her fetus. But only if the mother contracts the infection while she is pregnant or just a couple weeks before becoming pregnant. If a woman is infected prior to pregnancy, the parasite will be encysted in her tissues, but will not be actively dividing and spreading, so it cannot infect the baby. Only during the acute phase of infection is the baby at risk.Congenital Toxoplasmosis is not uncommon, affecting about 1 in every 10,000 births, or about 400 babies in the US each year. Well, that number really represents the babies born with birth defects, but some babies will not show symptoms for several years. The severity of the disease depends on when during the pregnancy the mother is infected, generally the earlier in pregnancy the more severe the damage to the fetus. If a woman is infected very early in pregnancy, the parasite usually causes abortion of the fetus. If infected within the first 6 months of pregnancy, the fetus may have damage to the brain. This picture on the right shows a baby with hydrocephalus, which is spinal fluid building up between the brain and the skull. This puts pressure on the developing brain, causing mental retardation. Infection of the eyes can cause blindness in babies infected early. If infected during the third trimester, a baby may not show any symptoms at birth, but could develop problems with the eyes in early childhood that can lead to blindness.

48

A: Presence of DNA. B: Presence of ß-glucan-containing cell walls.

C: Presence of cellulose. D: Presence of peptidoglycan cell walls.

CQ4: Becky’s Anti-Eukaryotic Medicines:

• Pyrimethamine, Sulfonamides: Interfere with enzymes used to make the folic acid needed to make thymine

and uracil nucleotides.

• Polyenes combine with a component of fungal and some bacterial membranes, disrupt and break them.

One of these drugs specifically affects one of the two eukaryotic suspects. Which test of Ellie’s blood would help

you tell which eukaryotic suspect she was infected with?

49

Part III: Viruses

• Becky and Ann are back at the dorm waiting for the results of more tests.

• “I’ve also got some tamiflu,” Becky volunteered. “I mean, what if those cells in the picture aren’t really making her sick. Maybe she just has the plain old flu.”

• “What do you mean?” Ann asked. What’s the difference?”

• “Flu is a virus,” Becky answers. “I’ve actually got two suspects that are viruses. They’re probably the most different from the prokaryotes and eukaryotes. They’re not even cells.”

Viruses

Not cells • Cannot reproduce alone

– hijacks a host cell to replicate itself – Composition

– Outer shell: repetitive protein often inserted into a lipid envelope (responsible for recognition and

infection of host cell.)

Viruses

• Size – Smallest Organisms (50nm)

– 100 times smaller than bacteria • Composition

– Protected interior that contains genetic material (DNA or RNA) with important protein enzymes

required for duplication.

52


4. Influenza Virus: Spread primarily through respiratory droplets from sneezing or coughing. Virus has single strand of RNA surrounded by phospholipids/protein envelope (80-120nm).

5. West Nile Virus: Spread by mosquitoes that have previously fed on infected birds. 20% of infected people show symptoms. Single stranded RNA, phospholipid/protein envelope (50nm).

Electron micrographs

53

CQ5: Match the description with the suspect. Identify the row below that best describes West

Nile Virus.

Circular DNA

Nucleus Divides asexually

Size Cell Wall

Sexual Reproduction

A + - + 1µm + - B - + + 10µm - + C - - - 0.1µm - - D - + + 5µm + +

54

Part IV: DNA Analysis

“Well, it isn’t viral,” Becky said, closing her cell phone. “No neuraminidase. But, they found some foreign DNA with the sequence: AACGTGGTCGTT. The closest match is a gene used to make ribosomes (rDNA). They are searching a huge DNA database of sequences to find the organism that has the closest match.”

55

A: Ellie’s nucleus ATGGTCTCAATG

B: Ellie’s mitochondria TTGGTCCGTCAG

C: Coxiella bacteria TTGGTCGGTCAG

D: Toxoplasma nucleus AACGTGGTAGTT

E: Cryptococcus nucleus ATGGTGGCAATG

CQ6: Foreign DNA sequence isolated from Ellie: ACGTGGTCGTT.

Which sequence is the best match with this foreign DNA?

56

Finale: Ellie’s Prognosis

“Well, Ellie’s responding well to the pyrimethamines that the doctors prescribed,” Becky commented to Ann while checking her email a few days later at the dorm.

“Yeah, and we’re lucky the cipro we took couldn’t harm our cells,” Ann replied. “We were so wrong! I’m never self-medicating again. Do you think we should warn the other students. They might have had contact with the kitten, too.”

“We don’t know if it was from cat poop,” Becky answered. “I learned that something like 25-40% of American adults are already infected with Toxoplasma gondii, and not because of their cats—usually it’s from eating raw meat. Plus, apparently the oocysts in fresh cat poop aren’t infectious for a couple of days. So, if you scoop the box right away you don’t have to worry.”

“So now I have to know how often the cat box is cleaned?! I don’t think I’m cut out for this job!” Ann moaned.

A: A prokaryotic cell.

B: A eukaryotic cell, but not a plant cell.

C: An animal cell, but not a protist cell.

D: Any eukaryotic cell.

E: A virus or a prokaryotic cell.

Answer: B

PQ3: An organism has the following: proteins, DNA, ribosomes, plasma membrane and mitochondria (among other structures.) Select the most inclusive answer for what type of organism it could be.

Parts of the Cell

• The plasma membrane is a selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell

• The general structure of a biological membrane is a double layer of phospholipids


Fig. 6-7 TEM of a plasma membrane

(a)

(b) Structure of the plasma membrane

Outside of cell

Inside of cell 0.1 µm

Hydrophilic region

Hydrophobic region

Hydrophilic region Phospholipid Proteins

Carbohydrate side chain

PresenterPresentation NotesFigure 6.7 The plasma membrane

• The logistics of carrying out cellular metabolism sets limits on the size of cells

• The surface area to volume ratio of a cell is critical

• As the surface area increases by a factor of n2, the volume increases by a factor of n3

• Small cells have a greater surface area relative to volume


Fig. 6-8 Surface area increases while

total volume remains constant

5

1 1

6 150 750

125 125 1

6 6 1.2

Total surface area [Sum of the surface areas (height × width) of all boxes sides × number of boxes]

Total volume [height × width × length × number of boxes]

Surface-to-volume (S-to-V) ratio [surface area volume]

PresenterPresentation NotesFigure 6.8 Geometric relationships between surface area and volume

A Panoramic View of the Eukaryotic Cell

• A eukaryotic cell has internal membranes that partition the cell into organelles

• Plant and animal cells have most of the same organelles

BioFlix: Tour Of An Animal Cell

BioFlix: Tour Of A Plant Cell


Fig. 6-9a

ENDOPLASMIC RETICULUM (ER)

Smooth ER Rough ER Flagellum

Centrosome

CYTOSKELETON: Microfilaments

Intermediate filaments

Microtubules

Microvilli

Peroxisome

Mitochondrion Lysosome

Golgi apparatus

Ribosomes

Plasma membrane

Nuclear envelope

Nucleolus

Chromatin

NUCLEUS

PresenterPresentation NotesFigure 6.9 Animal and plant cells—animal cell

Fig. 6-9b

NUCLEUS Nuclear envelope Nucleolus Chromatin

Rough endoplasmic reticulum

Smooth endoplasmic reticulum

Ribosomes

Central vacuole

Microfilaments Intermediate filaments Microtubules

CYTO- SKELETON

Chloroplast

Plasmodesmata Wall of adjacent cell

Cell wall

Plasma membrane

Peroxisome

Mitochondrion

Golgi apparatus

PresenterPresentation NotesFigure 6.9 Animal and plant cells—plant cell

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Concept 6.3: The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes

• The nucleus contains most of the DNA in a eukaryotic cell

• Ribosomes use the information from the DNA to make proteins


The Nucleus: Information Central

• The nucleus contains most of the cell’s genes and is usually the most conspicuous organelle

• The nuclear envelope encloses the nucleus, separating it from the cytoplasm

• The nuclear membrane is a double membrane; each membrane consists of a lipid bilayer


Fig. 6-10

Nucleolus Nucleus

Rough ER

Nuclear lamina (TEM)

Close-up of nuclear envelope

1 µm

1 µm

0.25 µm

Ribosome

Pore complex

Nuclear pore

Outer membrane Inner membrane Nuclear envelope:

Chromatin

Surface of nuclear envelope

Pore complexes (TEM)

PresenterPresentation NotesFigure 6.10 The nucleus and its envelope

• Pores regulate the entry and exit of molecules from the nucleus

• The shape of the nucleus is maintained by the nuclear lamina, which is composed of protein


• In the nucleus, DNA and proteins form genetic material called chromatin

• Chromatin condenses to form discrete chromosomes

• The nucleolus is located within the nucleus and is the site of ribosomal RNA (rRNA) synthesis


Ribosomes: Protein Factories

• Ribosomes are particles made of ribosomal RNA and protein

• Ribosomes carry out protein synthesis in two locations:

– In the cytosol (free ribosomes)

– On the outside of the endoplasmic reticulum or the nuclear envelope (bound ribosomes)


PresenterPresentation NotesFor the Cell Biology Video Staining of Endoplasmic Reticulum, go to Animation and Video Files.

Fig. 6-11

Cytosol

Endoplasmic reticulum (ER)

Free ribosomes

Bound ribosomes

Large subunit

Small subunit

Diagram of a ribosome TEM showing ER and ribosomes

0.5 µm

PresenterPresentation NotesFigure 6.11 Ribosomes

Concept 6.4: The endomembrane system regulates protein traffic and performs metabolic functions in the cell

• Components of the endomembrane system: – Nuclear envelope – Endoplasmic reticulum – Golgi apparatus – Lysosomes – Vacuoles – Plasma membrane

• These components are either continuous or connected via transfer by vesicles


The Endoplasmic Reticulum: Biosynthetic Factory

• The endoplasmic reticulum (ER) accounts for more than half of the total membrane in many eukaryotic cells

• The ER membrane is continuous with the nuclear envelope

• There are two distinct regions of ER:

– Smooth ER, which lacks ribosomes

– Rough ER, with ribosomes studding its surface


PresenterPresentation NotesFor the Cell Biology Video ER and Mitochondria in Leaf Cells, go to Animation and Video Files.

Fig. 6-12 Smooth ER

Rough ER Nuclear envelope

Transitional ER

Rough ER Smooth ER Transport vesicle

Ribosomes Cisternae ER lumen

200 nm

PresenterPresentation NotesFigure 6.12 Endoplasmic reticulum (ER)

Functions of Smooth ER

• The smooth ER

– Synthesizes lipids

– Metabolizes carbohydrates

– Detoxifies poison

– Stores calcium


Functions of Rough ER

• The rough ER

– Has bound ribosomes, which secrete glycoproteins (proteins covalently bonded to carbohydrates)

– Distributes transport vesicles, proteins surrounded by membranes

– Is a membrane factory for the cell


The Golgi Apparatus: Shipping and Receiving Center


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• http://media.pearsoncmg.com/bc/bc_campbell_biology_8/cellbiovideos/06_13ERToGolgiTraffic.html

PresenterPresentation NotesFor the Cell Biology Video ER to Golgi Traffic, go to Animation and Video Files.For the Cell Biology Video Golgi Complex in 3D, go to Animation and Video Files.For the Cell Biology Video Secretion From the Golgi, go to Animation and Video Files.

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Fig. 6-13

cis face (“receiving” side of Golgi apparatus) Cisternae

trans face (“shipping” side of Golgi apparatus)

TEM of Golgi apparatus

0.1 µm

PresenterPresentation NotesFigure 6.13 The Golgi apparatus

Lysosomes: Digestive Compartments

• A lysosome is a membranous sac of hydrolytic enzymes that can digest macromolecules

• Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids

Animation: Lysosome Formation


• Some types of cell can engulf another cell by phagocytosis; this forms a food vacuole

• A lysosome fuses with the food vacuole and digests the molecules

• Lysosomes also use enzymes to recycle the cell’s own organelles and macromolecules, a process called autophagy


PresenterPresentation NotesFor the Cell Biology Video Phagocytosis in Action, go to Animation and Video Files.

Fig. 6-14a Nucleus 1 µm

Lysosome

Lysosome

Digestive enzymes

Plasma membrane

Food vacuole

Digestion

(a) Phagocytosis

PresenterPresentation NotesFigure 6.14a Lysosome—phagocytosis

Fig. 6-14b Vesicle containing two damaged organelles

Mitochondrion fragment

Peroxisome fragment

Peroxisome

Lysosome

Digestion Mitochondrion Vesicle

(b) Autophagy

1 µm

PresenterPresentation NotesFigure 6.14b Lysosomes—autophagy

Vacuoles: Diverse Maintenance Compartments

• A plant cell or fungal cell may have one or several vacuoles


• Food vacuoles are formed by phagocytosis

• Contractile vacuoles, found in many freshwater protists, pump excess water out of cells

• Central vacuoles, found in many mature plant cells, hold organic compounds and water

Video: Paramecium Vacuole


Fig. 6-15

Central vacuole

Cytosol

Central vacuole

Nucleus

Cell wall

Chloroplast

5 µm

PresenterPresentation NotesFigure 6.15 The plant cell vacuole

The Endomembrane System: A Review

• The endomembrane system is a complex and dynamic player in the cell’s compartmental organization


Fig. 6-16-1

Smooth ER

Nucleus

Rough ER

Plasma membrane

PresenterPresentation NotesFigure 6.16 Review: relationships among organelles of the endomembrane system

Fig. 6-16-2

Smooth ER

Nucleus

Rough ER

Plasma membrane

cis Golgi

trans Golgi


Fig. 6-16-3

Smooth ER

Nucleus

Rough ER

Plasma membrane

cis Golgi

trans Golgi


Concept 6.5: Mitochondria and chloroplasts change energy from one form to another

• Mitochondria are the sites of cellular respiration, a metabolic process that generates ATP

• Chloroplasts, found in plants and algae, are the sites of photosynthesis

• Peroxisomes are oxidative organelles


PresenterPresentation NotesFor the Cell Biology Video ER and Mitochondria in Leaf Cells, go to Animation and Video Files.For the Cell Biology Video Mitochondria in 3D, go to Animation and Video Files.For the Cell Biology Video Chloroplast Movement, go to Animation and Video Files.

• Mitochondria and chloroplasts

– Are not part of the endomembrane system

– Have a double membrane

– Have proteins made by free ribosomes

– Contain their own DNA


Mitochondria: Chemical Energy Conversion

• Mitochondria are in nearly all eukaryotic cells

• They have a smooth outer membrane and an inner membrane folded into cristae

• The inner membrane creates two compartments: intermembrane space and mitochondrial matrix

• Some metabolic steps of cellular respiration are catalyzed in the mitochondrial matrix

• Cristae present a large surface area for enzymes that synthesize ATP


Fig. 6-17

Free ribosomes in the mitochondrial matrix

Intermembrane space Outer membrane

Inner membrane Cristae

Matrix

0.1 µm

PresenterPresentation NotesFigure 6.17 The mitochondrion, site of cellular respiration

Mitochondria

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Chloroplasts: Capture of Light Energy

• The chloroplast is a member of a family of organelles called plastids

• Chloroplasts contain the green pigment chlorophyll, as well as enzymes and other molecules that function in photosynthesis

• Chloroplasts are found in leaves and other green organs of plants and in algae


• Chloroplast structure includes:

– Thylakoids, membranous sacs, stacked to form a granum

– Stroma, the internal fluid


Fig. 6-18

Ribosomes

Thylakoid

Stroma

Granum

Inner and outer membranes

1 µm

PresenterPresentation NotesFigure 6.18 The chloroplast, site of photosynthesis

Peroxisomes: Oxidation

• Peroxisomes are specialized metabolic compartments bounded by a single membrane

• Peroxisomes produce hydrogen peroxide and convert it to water

• Oxygen is used to break down different types of molecules


Concept 6.6: The cytoskeleton is a network of fibers that organizes structures and activities in the cell

• The cytoskeleton is a network of fibers extending throughout the cytoplasm

• It organizes the cell’s structures and activities, anchoring many organelles

• It is composed of three types of molecular structures: – Microtubules – Microfilaments – Intermediate filaments


PresenterPresentation NotesFor the Cell Biology Video The Cytoskeleton in a Neuron Growth Cone, go to Animation and Video FilesFor the Cell Biology Video Cytoskeletal Protein Dynamics, go to Animation and Video Files.

Fig. 6-20

Microtubule

Microfilaments 0.25 µm

PresenterPresentation NotesFigure 6.20 The cytoskeleton

Roles of the Cytoskeleton: Support, Motility, and Regulation

• The cytoskeleton helps to support the cell and maintain its shape

• It interacts with motor proteins to produce motility

• Inside the cell, vesicles can travel along “monorails” provided by the cytoskeleton

• Recent evidence suggests that the cytoskeleton may help regulate biochemical activities


Fig. 6-21

Vesicle ATP

Receptor for motor protein

Microtubule of cytoskeleton

Motor protein (ATP powered)

(a)

Microtubule Vesicles

(b)

0.25 µm

PresenterPresentation NotesFigure 6.21 Motor proteins and the cytoskeleton

Components of the Cytoskeleton

• Three main types of fibers make up the cytoskeleton:

– Microtubules are the thickest of the three components of the cytoskeleton

– Microfilaments, also called actin filaments, are the thinnest components

– Intermediate filaments are fibers with diameters in a middle range


PresenterPresentation NotesFor the Cell Biology Video Actin Network in Crawling Cells, go to Animation and Video Files.For the Cell Biology Video Actin Visualization in Dendrites, go to Animation and Video Files.

Centrosomes and Centrioles

• In many cells, microtubules grow out from a centrosome near the nucleus

• The centrosome is a “microtubule-organizing center”

• In animal cells, the centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring


Fig. 6-22 Centrosome

Microtubule

Centrioles 0.25 µm

Longitudinal section of one centriole

Microtubules Cross section of the other centriole

PresenterPresentation NotesFigure 6.22 Centrosome containing a pair of centrioles

Cilia and Flagella • Microtubules control the beating of cilia and

flagella, locomotor appendages of some cells • Cilia and flagella differ in their beating patterns

Video: Chlamydomonas Video: Paramecium Cilia


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Fig. 6-23

5 µm

Direction of swimming

(a) Motion of flagella

Direction of organism’s movement

Power stroke Recovery stroke

(b) Motion of cilia 15 µm

PresenterPresentation NotesFigure 6.23a A comparison of the beating of flagella and cilia—motion of flagella

• Cilia and flagella share a common ultrastructure:

– A core of microtubules sheathed by the plasma membrane

– A basal body that anchors the cilium or flagellum

– A motor protein called dynein, which drives the bending movements of a cilium or flagellum

Animation: Cilia and Flagella


• Flagella and Cilia

• Cytoplasmic streaming is a circular flow of cytoplasm within cells

• This streaming speeds distribution of materials within the cell

• In plant cells, actin-myosin interactions and sol-gel transformations drive cytoplasmic streaming

Video: Cytoplasmic Streaming


Concept 6.7: Extracellular components and connections between cells help coordinate cellular activities

• Most cells synthesize and secrete materials that are external to the plasma membrane

• These extracellular structures include:

– Cell walls of plants

– The extracellular matrix (ECM) of animal cells

– Intercellular junctions


PresenterPresentation NotesFor the Cell Biology Video Ciliary Motion, go to Animation and Video Files.

Cell Walls of Plants

• The cell wall is an extracellular structure that distinguishes plant cells from animal cells

• Prokaryotes, fungi, and some protists also have cell walls

• The cell wall protects the plant cell, maintains its shape, and prevents excessive uptake of water

• Plant cell walls are made of cellulose fibers embedded in other polysaccharides and protein


• Plant cell walls may have multiple layers: – Primary cell wall: relatively thin and flexible – Middle lamella: thin layer between primary

walls of adjacent cells – Secondary cell wall (in some cells): added

between the plasma membrane and the primary cell wall

• Plasmodesmata are channels between adjacent plant cells


PresenterPresentation NotesFor the Cell Biology Video E-cadherin Expression, go to Animation and Video Files.

Fig. 6-28

Secondary cell wall Primary cell wall

Middle lamella

Central vacuole Cytosol Plasma membrane

Plant cell walls

Plasmodesmata

1 µm

PresenterPresentation NotesFigure 6.28 Plant cell walls

The Extracellular Matrix (ECM) of Animal Cells

• Animal cells lack cell walls but are covered by an elaborate extracellular matrix (ECM)

• The ECM is made up of glycoproteins such as collagen, proteoglycans, and fibronectin

• ECM proteins bind to receptor proteins in the plasma membrane called integrins


PresenterPresentation NotesFor the Cell Biology Video Cartoon Model of a Collagen Triple Helix, go to Animation and Video Files.For the Cell Biology Video Staining of the Extracellular Matrix, go to Animation and Video Files.For the Cell Biology Video Fibronectin Fibrils, go to Animation and Video Files.

Fig. 6-30

EXTRACELLULAR FLUID Collagen

Fibronectin

Plasma membrane

Micro- filaments

CYTOPLASM

Integrins

Proteoglycan complex

Polysaccharide molecule

Carbo- hydrates

Core protein

Proteoglycan molecule

Proteoglycan complex

PresenterPresentation NotesFigure 6.30 Extracellular matrix (ECM) of an animal cell, part 1

• Functions of the ECM: – Support – Adhesion – Movement – Regulation


Intercellular Junctions

• Neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through direct physical contact

• Intercellular junctions facilitate this contact

• There are several types of intercellular junctions – Plasmodesmata – Tight junctions – Desmosomes – Gap junctions


Plasmodesmata in Plant Cells

• Plasmodesmata are channels that perforate plant cell walls

• Through plasmodesmata, water and small solutes (and sometimes proteins and RNA) can pass from cell to cell


Fig. 6-31

Interior of cell

Interior of cell

0.5 µm Plasmodesmata Plasma membranes

Cell walls

PresenterPresentation NotesFigure 6.31 Plasmodesmata between plant cells

Tight Junctions, Desmosomes, and Gap Junctions in Animal Cells

• At tight junctions, membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid

• Desmosomes (anchoring junctions) fasten cells together into strong sheets

• Gap junctions (communicating junctions) provide cytoplasmic channels between adjacent cells

Animation: Tight Junctions

Animation: Desmosomes

Animation: Gap Junctions


Fig. 6-32

Tight junction

0.5 µm

1 µm Desmosome

Gap junction Extracellular matrix

0.1 µm

Plasma membranes of adjacent cells

Space between cells

Gap junctions

Desmosome

Intermediate filaments

Tight junction

Tight junctions prevent fluid from moving across a layer of cells

PresenterPresentation NotesFigure 6.32 Intercellular junctions in animal tissues

The Cell: A Living Unit Greater Than the Sum of Its Parts

• Cells rely on the integration of structures and organelles in order to function

• For example, a macrophage’s ability to destroy bacteria involves the whole cell, coordinating components such as the cytoskeleton, lysosomes, and plasma membrane


Fig. 6-33

PresenterPresentation NotesFigure 6.33 The emergence of cellular functions

Fig. 6-UN1a

Cell Component Structure Function

Concept 6.3 The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes

Nucleus Surrounded by nuclear envelope (double membrane) perforated by nuclear pores. The nuclear envelope is continuous with the endoplasmic reticulum (ER).

(ER)

Houses chromosomes, made of chromatin (DNA, the genetic material, and proteins); contains nucleoli, where ribosomal subunits are made. Pores regulate entry and exit os materials.

Ribosome Two subunits made of ribosomal RNA and proteins; can be free in cytosol or bound to ER

Protein synthesis

Fig. 6-UN1b

Cell Component Structure Function

Concept 6.4 The endomembrane system regulates protein traffic and performs metabolic functions in the cell

Endoplasmic reticulum (Nuclear envelope)

Golgi apparatus

Lysosome

Vacuole Large membrane-bounded vesicle in plants

Membranous sac of hydrolytic enzymes (in animal cells)

Stacks of flattened membranous sacs; has polarity (cis and trans faces)

Extensive network of membrane-bound tubules and sacs; membrane separates lumen from cytosol; continuous with the nuclear envelope.

Smooth ER: synthesis of lipids, metabolism of carbohydrates, Ca2+ storage, detoxifica- tion of drugs and poisons

Rough ER: Aids in sythesis of secretory and other proteins from bound ribosomes; adds carbohydrates to glycoproteins; produces new membrane

Modification of proteins, carbohydrates on proteins, and phospholipids; synthesis of many polysaccharides; sorting of Golgi products, which are then released in vesicles.

Breakdown of ingested substances cell macromolecules, and damaged organelles for recycling

Digestion, storage, waste disposal, water balance, cell growth, and protection

Fig. 6-UN1c

Cell Component

Concept 6.5 Mitochondria and chloroplasts change energy from one form to another

Mitochondrion

Chloroplast

Peroxisome

Structure Function

Bounded by double membrane; inner membrane has infoldings (cristae)

Typically two membranes around fluid stroma, which contains membranous thylakoids stacked into grana (in plants)

Specialized metabolic compartment bounded by a single membrane

Cellular respiration

Photosynthesis

Contains enzymes that transfer hydrogen to water, producing hydrogen peroxide (H2O2) as a by-product, which is converted to water by other enzymes in the peroxisome

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Golgi Brefeldin A is a drug that disrupts transport from the ER to the Golgi apparatus. What other organelles and membranes are affected?

– lysosomes, vacuoles, plasma membrane

– lysosomes, peroxisomes, plasma membrane

– vacuoles, mitochondria, plasma membrane

– lysosomes, vacuoles, nuclear membrane

– all intracellular organelles and membranes

– Answer: A

PresenterPresentation NotesAnswer: a

This question corresponds with Concept 6.4. It addresses student understanding of membrane flow and the continuity of the endomembrane system.

Microtubule Function Taxol, a drug approved for treatment of breast cancer, prevents depolymerization of microtubules. What cellular function that affects cancer cells more than normal cells might taxol interfere with? – maintaining cell shape

– cilia or flagella

– chromosome movements in cell division

– cell division (cleavage furrow formation)

– cytoplasmic streaming

– Answer: C

PresenterPresentation NotesAnswer: c

This question corresponds with Concept 6.5 and Table 6.1 and relates the cytoskeleton to cell division and cancer. It emphasizes that cytoskeletal elements have to be dynamic: Freezing the microtubules prevents the dynamic microtubule rearrangements, growth, and depolymerization required for cell division. It asks students to think about the differences between cancer cells and normal cells.

ECM in Plant and Animal Cells The difference in the structures of animal cell extracellular matrix and plant cell walls reflects what fundamental difference(s) in their adaptive strategies?

– Animal cells must move more than plant cells.

– Animal cells have to be more responsive to changes in their environment.

– Animal cells have to communicate with each other more than plant cells.

– all of the above

– Answer: A

PresenterPresentation NotesAnswer: a

This question corresponds with Concept 6.7. Plant cells may have to be even more responsive to environmental changes than animal cells, because animal cells can more easily relocate to a more hospitable environment, whereas plant cells can adapt only in place. Likewise, cell-to-cell signaling is just as important for plant development and adaptation as it is for animals.

• Under which of the following conditions would you expect to find a cell with a predominance of free ribosomes?

• A) a cell that is secreting proteins

• B) a cell that is digesting food particles

• C) a cell that is constructing its cell wall or extracellular matrix

• D) a cell that is producing cytoplasmic proteins

• Answer: D

• 4) Tay-Sachs disease is a human genetic abnormality that results in cells accumulating and becoming clogged with very large and complex lipids. Which cellular organelle must be involved in this condition?

• A) the Golgi apparatus

• B) membrane-bound ribosomes

• C) mitochondria

• D) the lysosome

• E) the endoplasmic reticulum

• Answer: D

• 5) The peroxisome gets its name from its interaction with hydrogen peroxide. If a liver cell is detoxifying alcohol and some other poisons, it does so by removal of hydrogen from the molecules.

• What, then, do the enzymes of the peroxisome do?

• A) combine the hydrogen with ATP

• B) use the hydrogen to break down hydrogen peroxide

• C) transfer the hydrogens to oxygen molecules

• D) transfer the harmful substances to the mitochondria

• Answer: C

• 6) The cell walls of bacteria, fungi, and plant cells and the extracellular matrix of animal cells are all external to the plasma membrane. Which of the following is a characteristic of all of theseracellular structures?

• A) They must block water and small molecules in order to regulate the exchange of matter and

• energy with their environment.

• B) They are composed of a mixture of lipids and carbohydrates.

• C) They must permit information transfer between the cell's cytoplasm and the nucleus.

• D) They are constructed of materials that are largely synthesized in the cytoplasm and then transported out of the cell.

• E) They must provide a rigid structure that maintains an appropriate ratio of cell surface area to volume.

• Answer: D

• 7) When a potassium ion (K+) moves from the soil into the vacuole of a cell on the surface of a root, it must pass through several cellular structures. Which of the following correctly describes the order in which these structures will be encountered by the ion?

• A) primary cell wall plasma membrane tonoplast cytoplasm vacuole

• B) tonoplast primary cell wall plasma membrane cytoplasm

• C) secondary cell wall plasma membrane primary cell wall cytoplasm tonoplast

• D) plasma membrane primary cell wall cytoplasm tonoplast

• E) primary cell wall plasma membrane cytoplasm tonoplast

• Answer: E

Chapter 6Overview: The Fundamental Units of LifeSlide Number 3Concept 6.1: To study cells, biologists use microscopes and the tools of biochemistry�Metric ReviewSlide Number 6Slide Number 7Slide Number 8Slide Number 9Slide Number 10Slide Number 11Slide Number 12Pictures of CellsSlide Number 14Cell FractionationPart I - Mysterious IllnessPart I - Mysterious IllnessPart I, continued…Becky’s TaskYour TaskConcept 6.2: Eukaryotic cells have internal membranes that compartmentalize their functionsComparing Prokaryotic and Eukaryotic CellsProkaryotesProkaryotesSlide Number 25Slide Number 26Slide Number 27Cancer�Below is a picture of two human cancer cells sitting next to each other right before they're about to divide into four cells. They're derived from the now famous "HeLa" line of cancer cells, which were taken from Henrietta Lacks in 1951 and used for medical research without her permission. "Understanding how cells divide is critical to understanding how cancerous cells multiply and take over," according to Dr. Andrews. �PQ1: To distinguish between prokaryotes and eukaryotes, we need to consider:PQ4: You have an infection caused by a prokaryotic pathogen. Which of the following would make a good choice for killing off the prokaryote without harming your cells?Becky’s Internet Search Results – List of SuspectsSlide Number 32Slide Number 33Slide Number 34Part II: Microscope AnalysisPart II, ContinuedSlide Number 37EukaryotesEukaryotesEukaryotic OrganellesEukaryotic OrganellesSlide Number 42Slide Number 43Slide Number 44Slide Number 45Slide Number 46Slide Number 47Slide Number 48Part III: VirusesVirusesVirusesBecky’s Internet Search Results – List of SuspectsSlide Number 53Part IV: DNA AnalysisCQ6: Foreign DNA sequence isolated from Ellie: ACGTGGTCGTT. ��Which sequence is the best match with this foreign DNA?Finale: Ellie’s PrognosisPQ3: An organism has the following: proteins, DNA, ribosomes, plasma membrane and mitochondria (among other structures.) Select the most inclusive answer for what type of organism it could be. Parts of the CellSlide Number 59Slide Number 60Slide Number 61A Panoramic View of the Eukaryotic CellSlide Number 63Slide Number 64Slide Number 65Concept 6.3: The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomesThe Nucleus: Information CentralSlide Number 68Slide Number 69Slide Number 70Ribosomes: Protein FactoriesSlide Number 72Concept 6.4: The endomembrane system regulates protein traffic and performs metabolic functions in the cellThe Endoplasmic Reticulum: Biosynthetic FactorySlide Number 75Functions of Smooth ERFunctions of Rough ERThe Golgi Apparatus: Shipping and �Receiving CenterSlide Number 79Lysosomes: Digestive CompartmentsSlide Number 81Slide Number 82Slide Number 83Vacuoles: Diverse Maintenance CompartmentsSlide Number 85Slide Number 86The Endomembrane System: A ReviewSlide Number 88Slide Number 89Slide Number 90Concept 6.5: Mitochondria and chloroplasts change energy from one form to anotherSlide Number 92Mitochondria: Chemical Energy ConversionSlide Number 94MitochondriaChloroplasts: Capture of Light EnergySlide Number 97Slide Number 98Peroxisomes: OxidationConcept 6.6: The cytoskeleton is a network of fibers that organizes structures and activities in the cellSlide Number 101Roles of the Cytoskeleton: Support, Motility, and RegulationSlide Number 103Components of the Cytoskeleton Slide Number 106 Slide Number 108Slide Number 109Slide Number 110Slide Number 111Slide Number 112Concept 6.7: Extracellular components and connections between cells help coordinate cellular activitiesCell Walls of PlantsSlide Number 115Slide Number 116The Extracellular Matrix (ECM) of Animal CellsSlide Number 118Slide Number 119Intercellular JunctionsPlasmodesmata in Plant CellsSlide Number 122Tight Junctions, Desmosomes, and Gap Junctions in Animal CellsSlide Number 124The Cell: A Living Unit Greater Than the Sum of Its PartsSlide Number 126Slide Number 127Slide Number 128Slide Number 129Slide Number 130Golgi��Brefeldin A is a drug that disrupts transport from the ER to the Golgi apparatus. What other organelles and membranes are affected?Microtubule Function �Taxol, a drug approved for treatment of breast cancer, prevents depolymerization of microtubules. What cellular function that affects cancer cells more than normal cells might taxol interfere with?ECM in Plant and Animal Cells�The difference in the structures of animal cell extracellular matrix and plant cell walls reflects what fundamental difference(s) in their adaptive strategies?Slide Number 134Slide Number 135Slide Number 136Slide Number 137Slide Number 138

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A Tour of the Cell - Useful Advice€¦ · Chapter 6 A Tour of the Cell . Overview: The Fundamental Units of Life • All organisms are made of cells • The cell is the simplest