MCB 104

Genetics, Genomics, Cell Biology

Xavier Darzacq

Craig T. Miller

David Bilder

Your GSIs
Kristen
Verster

Megan
McIntosh

Ella
Waters

Michael
Bronski

Please attend your assigned section

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 book
No cheating will be tolerated
Dont fall behind early. If you do, make sure you
use all resources (e.g. office hours, extra reading)
to strengthen your understanding before the next
test/quiz. There is no flexibility in final grading.

Part I Cell Biology

David Bilder

Lecture slides posted on bCourses

(right) before lecture

Office hours:
Fridays 10-11
LSA 348

A note on textbooks and reading:

The best textbook for these lectures is Alberts,
Essential Cell Biology, 4th edition.
The most
meaty chapters are 1 and 15-18, available for $9
ea. online. I will point out other chapters that are
generally relevant to the lecture material. Reading
the textbook, esp. before lecture, will help you get
more out of the class. Not all lecture material is
covered in the textbook. You are responsible for all
material covered in lecture; you are not
responsible for textbook material that is not
covered in lecture.

Genetics, Genomics & Cell Biology

What is Cell Biology?
Study of structure, function, and organization of
biomolecules 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
Goal:
Get a mental model of how a cell works

Notes for these lectures:

We will consider primarily eukaryotic cells
(mostly yeast and animals)
Level of resolution will be generally proteins
and 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)

Strategy:
Cell Organization
Cytoskeleton
Cell Division
Regulation of Cell Cycle
Intracellular Transport
Signaling
(Cancer, Disease)

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

Cell evolution - tree of life based on molecular phylogeny

(genome sequences)

3 Domains
Bacteria
Archaea
Eukaryotes

ALL LIFE
IS
CELLULAR

Bacteria

Archaea

Eukaryotes

Lactococcus lactis

Methanosarcina

Red blood cells, leukocytes, platelets

Cell size
cells are small,
but vary widely in size

Cell:
Bacteria
Yeast
Human
fibroblast

Radius (m):
0.5-1
2.5

Volume (fl):
1
60

25

5000

The scale of life:

Minimum resolvable
by electron microscope
Minimum resolvable
by light microscope
Minimum resolvable
by unaided human eye

You are
here

0.2 nm

2 nm

20 nm

ATOMS
MOLECULES

200 nm

2 m

20 m

ORGANELLES

0.2 mm

2 mm

2 cm

20 cm

ORGANS
CELLS

ANIMALS

2m

Seeing cells requires microscopes:

Concepts
1). Magnification: increase in size
2). Resolution:
r=distance by which two closely spaced objects can be
distinguished
r : wavelength of illumination
Light microscope: r ~200 nm
Electron microscope: r ~2 nm

3). Contrast: difference between object and

surroundings
[4). Signal to Noise]

Light microscopy:

Nucleus vs.
cytoplasm, PM

see differences
in refractive
index: allows
visualization of
structure

Max resolution: ~200 nm

Images from:
http://www.microscopyu.com/
http://nobelprize.org
Pollard, Cell Biology2e

Fritz Zernike
Nobel prize in physics 1953
For phase contrast

The scale of life:

Minimum resolvable
by electron microscope
Minimum resolvable
by light microscope
Minimum resolvable
by unaided human eye

You are
here

0.2 nm

2 nm

20 nm

ATOMS
MOLECULES

200 nm

2 m

20 m

ORGANELLES

0.2 mm

2 mm

2 cm

20 cm

ORGANS
CELLS

ANIMALS

2m

Electron microscopy:
Use higher of electron:
Max resolution: ~2 nm

TEM=transmission EM
ultrastructure
Heavy metal staining scatters
electrons, creates contrast

Albert Claude

Christian de Duve George Palade

Nobel Prize in Physiology or Medicine 1974

For their discoveries concerning the structural and functional organization of the cell
Images from: http://www.microscopyu.com/, http://nobelprize.org, ASCB

Cell organization: prokaryotes

Even simple cells have a high degree of internal
organization
No: organelles (nor nucleus)
Yes: compartments, cytoskeleton

Image from Lodish, Molecular Cell Biology 6e

Cell organization: eukaryotes

Membrane-bound organelles
Compartments
Cytoskeleton

Image from Lodish, Molecular Cell Biology 6e

Localizing specific molecules in cells

Fluorescence microscopy
Excitation light
(1)

Emission light
(2)

Fluorescent
molecule

Protein of
interest

2>1

Green Fluorescent Protein (GFP)

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)

Osamu Shimomura, Martin Chalfie and Roger Y. Tsien

Nobel Prize in Chemistry 2008
For the discovery and development of the green fluorescent protein, GFP.

Bacteria expressing
different fluorescent
proteins:

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

Live Drosophila egg

chambers

A picture of complexity: Cellular macromolecules

Nucleic acids (DNA, RNA)
Proteins (and complexes)
Lipids

Molecular
census in a
simple cell:
E. coli

Cells are extremely crowded

Space between molecules is ~size of molecules
Constant random collisions, interactions
Image from Phillips, Kondev and Theriot, Physical Biology of the Cell 1e

Advantages of compartmentalization and

organization
Provide distinct microenvironment
Sequester harmful molecules
Concentrate specific molecules
Enable regulation

A major way that the cell does this is through

using 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

Membranes are composed of amphipathic lipids

Phosphoglycerides

Sphingolipids
Polar
Head
group

Hydrophobic
tails
Images from Pollard, Cell Biology 2e

Cellular lipids spontaneously form bilayers

Due to shape and
amphipathic nature
Free energy (G) is
reduced when fatty acids
interact with each other
to exclude water

Image from Lodish, Molecular Cell Biology 6e

Composition of membranes
3. Cholesterol
(in animals)
Image from Pollard, Cell Biology 2e

Polar hydroxyl
Rigid steroid ring

Non-polar
Hydrophobic tail
Increases membrane stiffness, less fluidity

Membrane bilayers are spatially organized:

Subdomain
with specific
lipids

Exoplasm
(outside)

Two leaflets
(outer and
inner) have
different
compositions

Cytoplasm
(inside of cell)
Image from Pollard, Cell Biology 2e

Membranes are spatially organized in cells:

Exoplasmic leaflet
faces outside of cell
OR inside of
vesicle/organelle

Cytoplasmic leaflet
faces cytoplasm

Different organelles
enriched for
different lipids
Image from Lodish, Molecular Cell Biology 6e

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