Bilder.1.Cell Organization

7/25/2019 Bilder.1.Cell Organization

1/30

MCB 104

Genetics, Genomics, Cell Biology

Xavier Darzacq Craig T. Miller David Bilder


2/30

EllaWaters

KristenVerster

Your GSIs

MichaelBronskiMeganMcIntosh

Please attend your assigned section


3/30

Course information is on syllabus (bCourses)

Note grading info:3 exams Final is !cumulative

Quizzes and Mini Quizzes take place in section

Exams are closed bookNo cheating will be tolerated

Dont fall behind early. If you do, make sure youuse all resources (e.g. office hours, extra reading)to strengthen your understanding before the next

test/quiz. There is no flexibility in final grading.


4/30

Part I Cell Biology

David Bilder

Lecture slides posted on bCourses

(right) before lecture

Office hours:Fridays 10-11

LSA 348


5/30

A note on textbooks and reading:

The best textbook for these lectures is Alberts,Essential Cell Biology, 4th edition. The mostmeaty chapters are 1 and 15-18, available for $9ea. online. I will point out other chapters that are

generally relevant to the lecture material. Readingthe textbook, esp. before lecture, will help you getmore out of the class. Not all lecture material iscovered in the textbook. You are responsible for all

material covered in lecture; you are notresponsible for textbook material that is notcovered in lecture.


6/30

Goal:Get a mental model of how a cell works

Genetics, Genomics & Cell Biology

What is Cell Biology?Study of structure, function, and organization ofbiomolecules that make up the basic unit of life

Premise:The cell is the machine that the genome makes

to pass itself on to the next generation


7/30

Notes for these lectures:

We will consider primarily eukaryotic cells(mostly yeast and animals)

Level of resolution will be generally proteinsand macromolecular machines

(not so much protein structure, nor tissues)

We will generally consider the cell in isolation(vs. as a larger part of the organism)


8/30

Cell Organization

Cytoskeleton

Cell DivisionRegulation of Cell Cycle

Intracellular Transport

Signaling

(Cancer, Disease)

Strategy:


9/30

Outline for Today:

-cell evolution-cell size-observing cells: microscopy

-observing subcellular organization-a molecular census in cells-membranes: assembly and organization

ECB Chap 1, 11


10/30

Cell evolution - tree of life based on molecular phylogeny(genome sequences)

3 DomainsBacteriaArchaea

Eukaryotes

ALL LIFEIS

CELLULAR

BacteriaLactococcus lactis

ArchaeaMethanosarcina

EukaryotesRed blood cells, leukocytes, platelets


11/30

Cell: Radius (m): Volume (fl):

Bacteria

Yeast

Human

fibroblast

0.5-1

2.5

25

1

60

5000

Cell size cells are small,but vary widely in size


12/30

0.2 nm 2 nm 20 nm 200 nm 2 m 20 m 0.2 mm 2 mm 2 cm 20 cm 2 m

ATOMS

MOLECULES

ORGANELLES

CELLS

ORGANS

ANIMALS

Minimum resolvable

by unaided human eye

Minimum resolvableby light microscope

Minimum resolvable

by electron microscope

You are

here

The scale of life:


13/30

Seeing cells requires microscopes:

Concepts

1). Magnification: increase in size

2). Resolution:r=distance by which two closely spaced objects can bedistinguished

r !": wavelength of illumination

Light microscope: r ~200 nm

Electron microscope: r ~2 nm

3). Contrast: difference between object andsurroundings

[4). Signal to Noise]


14/30

Light microscopy:

Fritz ZernikeNobel prize in physics 1953

For phase contrast

Images from:

http://www.microscopyu.com/http://nobelprize.org

Pollard, Cell Biology2e

see differencesin refractive

index: allowsvisualization of

structure

Nucleus vs.cytoplasm, PM

Max resolution: ~200 nm


15/30

0.2 nm 2 nm 20 nm 200 nm 2 m 20 m 0.2 mm 2 mm 2 cm 20 cm 2 m

ATOMS

MOLECULES

ORGANELLES

CELLS

ORGANS

ANIMALS

Minimum resolvable

by unaided human eye

Minimum resolvableby light microscope

Minimum resolvable

by electron microscope

You are

here

The scale of life:


16/30

Albert Claude Christian de Duve George Palade

Nobel Prize in Physiology or Medicine 1974For their discoveries concerning the structural and functional organization of the cell

Electron microscopy:

Ima es from: htt ://www.microsco u.com/, htt ://nobel rize.or , ASCB

TEM=transmission EMultrastructure

Use higher"of electron:

Heavy metal staining scatterselectrons, creates contrast

Max resolution: ~2 nm


17/30

Cell organization: prokaryotes

Image from Lodish, Molecular Cell Biology 6e

Even simple cells have a high degree of internalorganization

No: organelles (nor nucleus)Yes: compartments, cytoskeleton


18/30

Cell organization: eukaryotes


Membrane-bound organellesCompartmentsCytoskeleton


19/30

Localizing specific molecules in cells

Fluorescence microscopy

Excitation light("1)

Emission light("2)

"2>"1Protein of

interest

Fluorescentmolecule


20/30

Comes from a jellyfish, Aequorea victoria

Gene and protein can be expressed in most organisms

Non-toxic! Glows autonomously in the living cell

Now many different colored variants of GFP or similar proteins(blue, yellow, red, green)

Green Fluorescent Protein (GFP)

Osamu Shimomura, Martin Chalfie and Roger Y. TsienNobel Prize in Chemistry 2008

For the discovery and development of the green fluorescent protein, GFP.


21/30

http://www.tsienlab.ucsd.edu/Images.htm

Bacteria expressing

different fluorescentproteins:

Live Drosophila egg

chambers


22/30

Molecularcensus in asimple cell:

E. coli

Image from Phillips, Kondev and Theriot, Physical Biology of the Cell 1e

Cells are extremely crowdedSpace between molecules is ~size of molecules

Constant random collisions, interactions

A picture of complexity: Cellular macromolecules

Nucleic acids (DNA, RNA)

Proteins (and complexes)Lipids


23/30

Advantages of compartmentalization and

organization

Provide distinct microenvironment

Sequester harmful moleculesConcentrate specific molecules

Enable regulation


24/30

A major way that the cell does this is throughusing membranes

(plasma membrane, organelle membranes)

*Container for cellular biochemistry*Gives structure to cell/organelle

*Fluidity within the plane

*Allow regulated permeability-small hydrophobic molecules (gases) easily

-small polar molecules (water) more slowly-large and charged molecules: not w/o help


25/30

Membranes are composed of amphipathic lipids

Images from Pollard, Cell Biology 2e

SphingolipidsPhosphoglycerides

Hydrophobictails

PolarHead

group


26/30


Cellular lipids spontaneously form bilayers

Due to shape andamphipathic nature

Free energy (#G) isreduced when fatty acidsinteract with each other

to exclude water


27/30

Composition of membranes

Image from Pollard, Cell Biology 2e

3. Cholesterol (in animals)

Polar hydroxyl

Rigid steroid ring

Non-polarHydrophobic tail

Increases membrane stiffness, less fluidity


28/30

Membrane bilayers are spatially organized:

Image from Pollard, Cell Biology 2e

Cytoplasm(inside of cell)

Exoplasm(outside)

Two leaflets(outer and

inner) have

different

compositions

Subdomain

with specificlipids


29/30

Membranes are spatially organized in cells:


Exoplasmic leafletfaces outside of cell

OR inside of

vesicle/organelle

Cytoplasmic leafletfaces cytoplasm

Different organellesenriched for

different lipids


30/30

https://www.youtube.com/watch?v=wJyUtbn0O5Y

Documents

Bilder.1.Cell Organization