Chapter 7 A Tour of the Cell - Quia

Chapter 7

• A Tour of the Cell

How Big is a ... ?

microscopes

• Glass lenses were invented in Middle East

• Came to Europe after crusades

• 1600- 1700’s – compound two lenses 1,000 x upper limit

1665 – Robert Hooke found dead “cells” in cork

Molecular Expressions Microscopy Primer: Museum of

Microscopy - Hooke's Microscope

1673 – Anton van Leeuwenhoek observed microscopic living organisms “animicules”

1824– Henri Dutrochet – all living things are made of cells

1831 – Robert Brown (the Brownian motion guy)– observed the nucleus

1838 - Schleiden- all plants are made of cells

1839- Schwann - animals are made of

cells

SchleidenSchwann

1850- Louis Pasteur – pasteurization (of wine)

1855- Dr. Virchow- physician- cells come from preexisting cells

1860s Civil War soldiers died from infections

The Cell Theory

1. 1. All living things are composed of one or

more cells

2. The cell is the basic unit of structure and

function

1. 3.All cells come from preexisting cells

1950’s Electron microscope (EM)-thousands of times more powerful

but not alive (TEM)

1970’s Scanning em.-(SEM) 3d images

1980’s - scanning tunneling EM- you can

see individual atoms and

push them around

So the

Japanese

pushed CO

Cell Fractionation

• Is used to separate the various parts of cells for further study.

• An example of reductionism.

• You blend the cells to break them open and spin them down to separate heavier parts.

TWO CELL TYPES

1) Prokaryote cells

• 1) Prokaryote cells (no nucleus) before nucleus

• Domains Eubacteria and Archaea

• - Bacteria Kingdom Monera

• - single celled

2) Eukaryotic cells (has nucleus)

•

• Domain Eukarya

• - membrane bound organelles

• Kingdom

– Protists Protista

• fungus Fungi

• plants Plantae

• animals Animalia

Limits to cell size

• Lower limit to cell size:

• The cell must be big enough to contain DNA, RNA and several ribosomes.

20 to 100 nanometer

Upper Limits to Cell Size: The cell must be small because:

1) Diffusion- materials (H20 and CO2) can only diffuse so far so fast

•

• 2) DNA- controls cell functions bigger cells either split or have many nuclei.

•

• Most importantly

• 3) Surface area to volume ratio

Surface Area vs. Volume Ratio

0

1

2

3

4

5

6

71 3 5 7 9

11

13

15

Size of Object

Rati

o

Cube

Sphere

Long cylinder

Squat cylinder

Surface Area to Volume Ratio

0

500

1000

1500

1 5 9 1

3

1

7

Size of Cell

Ra

tio

SA

:V X

:1 Series1

Cube

sphere

tall cylinder

squat cylinder

Parts of the Eukaryotic Cell

• Cells are compartmentalized by membranes to allow the many different reactions to occur simultaneously. Many reactions occur in the membrane lining.

• Organelles - are specialized internal structures.

Prokaryote

bacteria cellsTypes of cells

Eukaryote

animal cells

- no organelles

- organelles

Eukaryote

plant cells

Why organelles?• Specialized structures

– specialized functions

• cilia or flagella for locomotion

• Containers

– partition cell into compartments

– create different local environments

• separate pH, or concentration of materials

– distinct & incompatible functions

• lysosome & its digestive enzymes

• Membranes as sites for chemical reactions

– unique combinations of lipids & proteins

– embedded enzymes & reaction centers

• chloroplasts & mitochondria

mitochondria

chloroplast

Golgi

ER

Cells gotta work to live! • What jobs do cells have to do?

– make proteins

• proteins control everycell function

– make energy

• for daily life

• for growth

– make more cells

• growth

• repair

• renewal

Proteins do all the work!

cells

DNA

proteins

organism

Repeat after me…Proteins do all the work!

Cells functions • Building proteins

– read DNA instructions

– build proteins

– process proteins

• folding

• modifying– removing amino acids

– adding other molecules

» e.g, making glycoproteinsfor cell membrane

– address & transport proteins

Building Proteins

• Organelles involved– nucleus

– ribosomes

– endoplasmic reticulum (ER)

– Golgi apparatus

– vesicles

nucleus ribosome ERGolgi

apparatusvesicles

The Protein Assembly Line

nuclearpores

nuclearpore

nuclear envelope

nucleolus

histone protein

chromosome

DNA

• Function

– protects DNA

• Structure

– nuclear envelope

• double membrane

• membrane fused in spots to create pores– allows large macromolecules to pass through

Nucleus

What kind of molecules need to pass through?

DNA

NucleusmRNA

nuclearmembrane

smallribosomalsubunit

largeribosomalsubunit

cytoplasm

mRNA

nuclear pore

production of mRNA

from DNA in nucleus

mRNA travels from

nucleus to ribosome in

cytoplasm through

nuclear pore

1

2

Nucleolus

• Function

– ribosome production

• build ribosome subunits from rRNA & proteins

• exit through nuclear pores to cytoplasm & combine to form functional ribosomes

smallsubunit

large subunit

ribosome

rRNA &proteins

nucleolus

smallsubunit

largesubunitRibosomes

• Function

– protein production

• Structure

– rRNA & protein

– 2 subunits combine 0.08mm

Ribosomes

RoughER

SmoothER

membrane proteins

Types of Ribosomes• Free ribosomes

– suspended in cytosol

– synthesize proteins that function in cytosol

• Bound ribosomes

– attached to endoplasmic reticulum

– synthesize proteins for export or for membranes

Endoplasmic Reticulum• Function

– processes proteins

– manufactures membranes

– synthesis & hydrolysis of many compounds

• Structure

– membrane connected to nuclear envelope & extends throughout cell

Types of ER

rough smooth

Rough ER function

• Produce proteins for export out of cell– protein secreting cells

– packaged into transport vesicles for export

Which cellshave lot of rough ER?

Smooth ER function

• Membrane production

• Many metabolic processes

– synthesis

• synthesize lipids – oils, phospholipids, steroids & sex hormones

– hydrolysis

• hydrolyze glycogen into glucose– in liver

• detoxify drugs & poisons– in liver

– ex. alcohol & barbiturates

Membrane Factory

• Build new membrane– synthesize

phospholipids• builds membranes

– ER membrane expands• bud off & transfer to

other parts of cell that need membranes

Synthesizing proteins

cytoplasm

cisternalspace

mRNA

ribosome

membrane ofendoplasmic reticulum

polypeptide

signalsequence

ribosome

Golgi Apparatus

Which cellshave lots of Golgi?

transport vesicles

secretoryvesicles

• Function

– finishes, sorts, tags & ships cell products

• like “UPS shipping department”

– ships products in vesicles

• membrane sacs

• “UPS trucks”

Golgi Apparatus

Vesicle transport

vesiclebuddingfrom roughER

fusionof vesiclewith Golgiapparatus

migratingtransportvesicle

protein

ribosome

DNA

RNA

ribosomes

endoplasmic

reticulum

vesicle

Golgi

apparatus

vesicle

proteinon its way!

protein finishedprotein

Making Proteins

TO:

TO:

TO:

TO:

nucleus

proteins

transportvesicle

Golgiapparatus

vesicle

smooth ER

rough ER

nuclear pore

nucleus

ribosome

cellmembrane protein secreted

cytoplasm

Making proteinsPutting it together…

Lysosomes

small food

particle

vacuole

digesting food

lysosomes

• Function

– digest food

– clean up & recycle• digest broken

organelles

• Structure

– membrane sac of digestive enzymes

digesting brokenorganelles

When things go bad…

• Diseases of lysosomes are often fatal– digestive enzyme not working in lysosome

– picks up biomolecules, but can’t digest one

• lysosomes fill up with undigested material

– grow larger & larger until disrupts cell & organ function

• lysosomal storage diseases– more than 40 known diseases

• example:Tay-Sachs diseasebuild up undigested fat in brain cells

Phagocytosis macrophages white blood cells

• Autophagy – recycling your own stuff

• Lysosomes absorb and digest stuff in cells.

• Liver cells recycle ½ of all macromolecules everyday.

But sometimes cells need to die…• Lysosomes can be used to kill cells when they

are supposed to be destroyed

– some cells have to die for proper development in an organism

• apoptosis– “auto-destruct” process

– lysosomes break open & kill cell

• ex: tadpole tail gets re-absorbed when it turns into a frog

• ex: loss of webbing between your fingers during fetal development

Fetal development

15 weeks

6 weeks

syndactyly

Making Energy

• Cells must convert incoming energy to forms that they can use for work

– mitochondria:from glucose to ATP

– chloroplasts:from sunlight to ATP & carbohydrates

• ATP = active energy

• carbohydrates = stored energy

+

ATP

ATP

Mitochondria & Chloroplasts

• Important to see the similarities

– transform energy

• generate ATP

– double membranes = 2 membranes

– semi-autonomous organelles

• move, change shape, divide

– internal ribosomes, DNA & enzymes

Mitochondria

• Function

– cellular respiration

– generate ATP

• from breakdown of sugars, fats & other fuels

• in the presence of oxygen

– break down larger molecules into smaller to generate energy = catabolism

– generate energy in presence of O2 = aerobic respiration

Mitochondria• Structure

– 2 membranes• smooth outer membrane

• highly folded inner membrane

– cristae

– fluid-filled space between 2 membranes

– internal fluid-filled space• mitochondrial matrix

• DNA, ribosomes & enzymes

Why 2 membranes?

increase surface area for membrane-bound

enzymes that synthesize ATP

Mitochondria

Membrane-bound Enzymes

glucose + oxygen carbon + water + energydioxide

C6H12O6 6O2 6CO2 6H2O ATP + + +

Dividing Mitochondria

Who else divides like

that?

What does this tell us about the

evolution of eukaryotes?

Mitochondria• Almost all eukaryotic cells have mitochondria

– there may be 1 very large mitochondrion or 100s to 1000s of individual mitochondria

– number of mitochondria is correlated with aerobic metabolic activity• more activity = more energy

needed = more mitochondria

What cells would

have a lot of

mitochondria?

active cells:

• muscle cells

• nerve cells

Mitochondria are everywhere!!

animal cells plant cells

Chloroplasts

• Chloroplasts are plant organelles

– class of plant structures = plastids

• amyloplasts– store starch in roots & tubers

• chromoplasts– store pigments for fruits & flowers

• chloroplasts– store chlorophyll & function

in photosynthesis

– in leaves, other green structures of plants & in eukaryotic algae

Chloroplasts

• Structure– 2 membranes

– stroma = internal fluid-filled space

• DNA, ribosomes & enzymes

• thylakoids = membranous sacs where ATP is made

• grana = stacks of thylakoids

Why internal sac membranes?

increase surface area for

membrane-bound enzymes that

synthesize ATP

Membrane-bound Enzymes

+ water + energy glucose + oxygencarbondioxide

6CO2 6H2O C6H12O6 6O2lightenergy

+ ++

Chloroplasts

• Function

– photosynthesis

– generate ATP & synthesize sugars

• transform solar energy into chemical energy

• produce sugars from CO2 & H2O

• Semi-autonomous• moving, changing shape & dividing

• can reproduce by pinching in two

Who else divides like

that?

bacteria!

Chloroplasts

Why are chloroplasts green?

Mitochondria & chloroplasts are different

• Organelles not part of endomembrane system

• Grow & reproduce

– semi-autonomous organelles

• Proteins primarily from free ribosomes in cytosol & a few from their own ribosomes

• Own circular chromosome

– directs synthesis of proteins produced by own internal ribosomes• ribosomes like bacterial ribosomes

Who else has a circular chromosome not

bound within a nucleus?

bacteria

Food & water storage

plant cells

central vacuole

contractile

vacuole

food vacuoles

animal cells

Vacuoles & vesicles

• Function

– little “transfer ships”

• Food vacuoles

– phagocytosis, fuse with lysosomes

• Contractile vacuoles

– in freshwater protists, pump excess H2O out of cell

• Central vacuoles

– in many mature plant cells

Cytoskeleton

• Function

– structural support• maintains shape of cell

• provides anchorage for organelles– protein fibers

» microfilaments, intermediate filaments, microtubules

– motility• cell locomotion

• cilia, flagella, etc.

– regulation

• organizes structures & activities of cell

actin

microtubule

nuclei

Cytoskeleton

Centrioles • Cell division

– in animal cells, pair of centriolesorganize microtubules• spindle fibers

– guide chromosomes in mitosis

Cells need to make more cells!• Making more cells

– to replace, repair & grow, the cell must…• copy their DNA

• make extra organelles

• divide the new DNA & new

organelles between 2 new

“daughter” cells

– organelles that do this work…• nucleus

• centrioles

Centrioles

• Function– help coordinate cell division

• Structure– one pair in each cell

– “motor” proteins

Putting it all together

animal cells plant cells

Chapter 8

Membrane Structure and Function

Cell Membrane A. Phospholipid bilayer

AMPHIPATHIC molecule

1. polar head (hydrophillic)

2 nonpolar tails (hydrophobic)

Phospholipids will form layers and bilayers in water

Arranged as a Phospholipid bilayer

polarhydrophilicheads

nonpolarhydrophobictails

polarhydrophilicheads

• Serves as a cellular barrier / border

H2Osugar

lipids

salt

waste

impermeable to polar molecules

Freeze fracturing

revealed the structure

Types of movement

Studies with mouse cells showed that the lipids can move, think

ping pong balls on a pool.

Trans-membrane

protein

Membranes have

sidedness (inside versus

outside)

Overview• Cell membrane separates living cell from nonliving

surroundings

– thin barrier = 8nm thick

• Controls traffic in & out of the cell

– selectively permeable

– allows some substances to cross more easily than others• hydrophobic vs hydrophilic

• Made of phospholipids, proteins & other macromolecules

Membrane is a collage of proteins & other molecules embedded in the fluid matrix of the lipid bilayer

Extracellular fluid

Cholesterol

Cytoplasm

Glycolipid

Transmembraneproteins

Filaments ofcytoskeleton

Peripheralprotein

Glycoprotein

Phospholipids

Membrane fat composition varies• Fat composition affects flexibility

– membrane must be fluid & flexible

• about as fluid as thick salad oil

– % unsaturated fatty acids in phospholipids

• keep membrane less viscous

• cold-adapted organisms, like winter wheat – increase % in autumn

– cholesterol in membrane

Membrane Proteins• Proteins determine membrane’s specific functions

– cell membrane & organelle membranes each have unique

collections of proteins

• Membrane proteins:

– peripheral proteins

• loosely bound to surface of membrane

• cell surface identity marker (antigens)

– integral proteins• penetrate lipid bilayer, usually across whole membrane

• transmembrane protein

• transport proteins

– channels, permeases (pumps)

2007-2008

Why areproteins the perfect molecule to build structures in the cell membrane?

Classes of amino acidsWhat do these amino acids have in common?

nonpolar & hydrophobic

Classes of amino acidsWhat do these amino acids have in common?

polar & hydrophilic

I like thepolar onesthe best!

Proteins domains anchor molecule• Within membrane

– nonpolar amino acids • hydrophobic

• anchors protein into membrane

• On outer surfaces of membrane

– polar amino acids

• hydrophilic

• extend into extracellular fluid & into cytosol

Polar areasof protein

Nonpolar areas of protein

NH2

H+

COOH

Cytoplasm

Retinalchromophore

Nonpolar(hydrophobic)a-helices in thecell membrane H+

Porin monomer

b-pleated sheets

Bacterialoutermembrane

proton pump channel

in photosynthetic bacteria

water channel

in bacteria

function through

conformational change =

shape change

Examples

Many Functions of Membrane Proteins

Outside

Plasmamembrane

Inside

Transporter Cell surfacereceptor

Enzyme

activity

Cell surface identity marker

Attachment to thecytoskeleton

Cell adhesion

Membrane carbohydrates • Play a key role in cell-cell recognition

– ability of a cell to distinguish one cell from another

• antigens

– important in organ & tissue development

– basis for rejection of foreign cells by immune system

Diffusion• 2nd Law of Thermodynamics

governs biological systems– universe tends towards disorder (entropy)

Diffusion

movement from high low concentration

Diffusion• Move from HIGH to LOW concentration

– “passive transport”

– no energy needed

diffusion osmosis

movement of water

Diffusion across cell membrane• Cell membrane is the boundary between

inside & outside…

– separates cell from its environment

INfood

carbohydrates

sugars, proteins

amino acids

lipids

salts, O2, H2O

OUTwaste

ammonia

salts

CO2

H2O

products

cell needs materials in & products or waste out

IN

OUT

Can it be an impenetrable boundary? NO!

Diffusion through phospholipid bilayer

• What molecules can get through directly?– fats & other lipids

inside cell

outside cell

lipid

salt

aa H2Osugar

NH3

What molecules can

NOT get through

directly?

polar molecules

H2O

ions

salts, ammonia

large molecules

starches, proteins

Channels through cell membrane• Membrane becomes semi-permeable with

protein channels

– specific channels allow specific material across cell membrane

inside cell

outside cell

sugaraaH2O

saltNH3

Facilitated Diffusion• Diffusion through protein channels

– channels move specific molecules across cell membrane

– no energy needed

“The Bouncer”

open channel = fast transport

facilitated = with help

high

low

2007-2008

The Special Case of Water

Movement of water across the cell membrane

Osmosis is diffusion of water

• Water is very important to life, so we talk about water separately

• Diffusion of water from high concentration of water to low concentration of water

– across a semi-permeable membrane

Concentration of water• Direction of osmosis is determined by

comparing total solute concentrations

– Hypertonic - more solute, less water

– Hypotonic - less solute, more water

– Isotonic - equal solute, equal water

hypotonic hypertonic

water

net movement of water

freshwater balanced saltwater

Managing water balance• Cell survival depends on balancing water

uptake & loss

Managing water balance• Isotonic

– animal cell immersed in mild salt solution

• example:blood cells in blood plasma

• problem: none

– no net movement of water» flows across membrane equally, in

both directions

– volume of cell is stable

balanced

Managing water balance• Hypotonic

– a cell in fresh water

• example: Paramecium

• problem: gains water,

swells & can burst

– water continually enters

Paramecium cell

• solution: contractile vacuole

– pumps water out of cell

– ATP

– plant cells• turgid

freshwater

ATP

Water regulation

• Contractile vacuole in Paramecium

ATP

Managing water balance• Hypertonic

– a cell in salt water

• example: shellfish

• problem: lose water & die

• solution: take up water or pump out salt

– plant cells• plasmolysis = wilt

saltwater

Aquaporins• Water moves rapidly into & out of cells

– evidence that there were water channels

1991 | 2003

Peter AgreJohn Hopkins

Roderick MacKinnonRockefeller

Cell (compared to beaker) hypertonic or hypotonic

Beaker (compared to cell) hypertonic or hypotonic

Which way does the water flow? in or out of cell

.05 M .03 M

Osmosis…

Active Transport

“The Doorman”

conformational change

• Cells may need to move molecules against concentration gradient– shape change transports solute from

one side of membrane to other

– protein “pump”

– “costs” energy = ATP

ATP

low

high

symportantiport

Active transport• Many models & mechanisms

ATP ATP

Getting through cell membrane• Passive Transport

– Simple diffusion• diffusion of nonpolar, hydrophobic molecules

– lipids

– high low concentration gradient

– Facilitated transport• diffusion of polar, hydrophilic molecules

• through a protein channel– high low concentration gradient

• Active transport– diffusion against concentration gradient

• low high

– uses a protein pump

– requires ATPATP

Transport summary

simplediffusion

facilitated

diffusion

active

transport

ATP

How about large molecules?• Moving large molecules into & out of cell

– through vesicles & vacuoles

– endocytosis

• phagocytosis = “cellular eating”

• pinocytosis = “cellular drinking”

– exocytosis

exocytosis

Endocytosis

phagocytosis

pinocytosis

receptor-mediated

endocytosis

fuse with

lysosome for

digestion

non-specific

process

triggered by

molecular

signal

Sodium – Potassium Pump

Cotransport

Vacuoles in plants

• Functions

– storage

• stockpiling proteins or inorganic ions

• depositing metabolic byproducts

• storing pigments

• storing defensive compounds against herbivores

• selective membrane

– control what comes in or goes out

Peroxisomes

• Other digestive enzyme sacs

– in both animals & plants

– breakdown fatty acids to sugars

• easier to transport & use as energy source

– detoxify cell

• detoxifies alcohol & other poisons

– produce peroxide (H2O2)

• must breakdown

H2O2 H2O