Cell Biology

with Dr. Kirby

 Roadmap for the course
Week Days Topics Reading Office: 29 aleph.3.7D
1. 13-15 Mar Cells as fundamental units of life Chapters 1, 2
Chemistry of cells Meetings by appointment
2. 20-22 mar Energy, catabolism, and anabolism Chapter 3 (live or Zoom)
3. 27-29 Mar Proteins: Structure and function Chapter 4
4. 3 Apr Chromosomes Chapters 5, 6 michaelki@ariel.ac.il
17 Apr DNA replication, recombination, and repair
5. 19 Apr Gene expression: DNA to protein Chapter 7
6. 24-26 Apr Control of gene expression Chapters 8, 10
Gene cloning • 1400-1600
7.
8.
1-3 May
8-10 May
Membranes
How cells obtain resources and use energy
Chapter 11
Chapters 12, 13, 14
M • 11.3.17
9. 15-17 May Intracellular transport Chapter 15
10. 22-24 May Cell signaling Chapter 16
11. 29-31 May Cell cycle and mitosis Chapters 17, 18
• 1100-1400
12.
13.
5-7 Jun
11-14 Jun
Meiosis
Cellular cooperation: Tissues and organs
Chapter 19
Chapter 20 W • 08.2.04
Essential Cell Biology, 5th Edition. Alberts, Hopkin, Johnson, Morgan, Raff, Roberts, and Walter
 What is life?
1. Higher negative entropy than inanimate
objects
2. Possess homeostatic mechanisms to
maintain a stable internal environment
3. Reproduce
4. Display development
5. Gather and transform resources
6. Respond to stimuli
7. Display adaptation
Shapes of cells are tailored
to their function
• Cells vary in size
• 0.2 μm (Bacteria: Mycoplasma gallicepticum)

• 10 cm (Viridiplantae: Caulerpa taxifolia)

• [that’s a 500,000x difference]

• Vary greatly in morphology

• Size and morphology can change over time

 All cells have similar chemistry
(but not identical)
• All cells use DNA for data storage
• Gene structure differs between prokaryotes
and eukaryotes (but more on that later)

• All cells use the same 4 DNA bases for

coding: ATGC

• All cells use the same DNA/RNA codon

set (codes) for amino acids

• All cells process gene expression in the

same basic manner

• All cells evolved from an ancestral cell

Why are most cells small?
• Good physics
• Small spheres have a higher
surface area:volume ratio
than larger spheres

Easier to understand with cubes…

Which of these equal volumes has the greatest surface area?

Q: What advantage is a greater surface area?

A: More interaction with outside world
 Scale
How small is small?
Please review panel 1-1
(pp. 12-13): types of
microscopes
Cells
• Come in 2 “flavors”
• Prokaryotic (“before nut”: no nucleus)
• Eukaryotic (“good nut”: true nucleus)

• Eukaryotic cells have 3 basic parts:

• Plasma membrane
• Cytoplasm
• Nucleus
 membrane envelope
DNA with no
Nucleoid: Jumble of
Prokaryotes
BACTERIA

common ARCHAEA
ancestor
(first cells)

membrane)
nuclear envelope (a.k.a. lipid
Nucleus: DNA enclosed in a
Protists

Photosynthetic
protist

Eukaryotes
Plants
cell with nucleus

EUKARYA
Fungi

Heterotrophic
Protist Animals
common ancestor

Past Present
Time
Descent with modification
...and now for: Cell Anatomy 101
Prokaryotes
• No nuclear envelope
• Single-celled organisms
• Most diverse and numerous cells on
Earth
• Have 1-2 cell membranes and a cell wall
• Reproduce through binary fission
• Can exchange genetic material
(prokaryotic “sex”)
• Some live free in the environment
(decomposers, autotrophs), others are
intracellular parasites of eukaryotes
• Share ancient ancestry with
mitochondria (more on those later)
• Classified in two domains: bacteria and
archaea
Eukaryotes
• Every living thing that is not a Bacterium
or Archaean
• Unicellular to multicellular
• Nuclear envelope
• Organelles
• Contain descendants of bacterial
ancestors
• Mitochondria: all species
Well... not Monocercomonoides sp.
• Chloroplasts: autotrophs
• Reproduction is more complex (asexual,
sexual), but still involves binary fission
• Live free in the environment
(heterotrophs, autotrophs, detritivores, Animal Cell
decomposers) or as parasites
Eukaryotes: the membrane-bound parts
Nucleus
• Most prominent organelle (easiest to see)
• Information storehouse containing DNA
(most of the cell genome)
• DNA is organized into chromosomes
• Only visible when cells are dividing
• Otherwise, DNA appears granular
• Enclosed in a double lipid membrane
(nuclear envelope)
• Also contains a Nucleolus (starting material
for making ribosomes as well as other
functions... more on that later)
Eukaryotes: the membrane-bound parts
Endoplasmic Reticulum (ER)
• An extension of the outer
membrane of the nucleus
• Comes in 2 fun flavors!
• Rough ER (RER)
• Manufacturing center for proteins
• A docking location for ribosomes (more
on those later)
• Smooth ER (SER)
• New membrane synthesis
• Detoxification enzymes
Eukaryotes: the membrane-bound parts
Golgi Apparatus (or body)
• Receives proteins made in the RER
• Modifies proteins
• Acts like a central post office
• Address labels: carbohydrate tags
• Proteins sent here destined for either
• Secretion (goes outside the cell)
• Transport to other organelles
• Transport to cell membrane
Eukaryotes: the membrane-bound parts
Mitochondria
• The Power plant: Makes energy for the cell
• Makes ATP (more on that later)
• Membrane potentials of about 150 mV
• Come in many shapes and sizes, depending
on cell type
• Contain a portion of the cell genome
• Ancestors were bacteria (gene structure is
prokaryote)
• Can independently divide... like bacteria
• Enclosed in a double lipid membrane (like
many bacteria)
Eukaryotes: the membrane-bound parts
Lysosomes & Peroxisomes
• Lysosomes
• The recycling plant
• Small, irregular organelles that
digest gathered resources, waste
products, and decommission
broken organelles
• Peroxisomes
• Use H2O2 to break down toxins
• Have oxidating enzymes that
assist metabolism
Eukaryotes: the membrane-bound parts
...and loads of membrane
vesicles

Numerous small membrane-bound

vesicles are used to transport materials
around the cell
Eukaryotes: some of the other stuff
Cytosol
• Aqueous “gel”
• Packed with proteins,
carbohydrates, amino acids,
nucleic acids, fatty acids, ions
Eukaryotes: some of the other stuff
Cytoskeleton
• Comprised of 3 types of elements:
• Microtubules (~25 nm wide)
• Intermediate filaments (~10 nm wide)
• Microfilaments (~7 nm wide)
• The railroad system of the cell
• Moves freight around the cell
• Guideways for intracellular transport
proteins to move products
• Participates in cell signaling
• The skeleton of the cell
• Provides structural support
• Attachments for organelles & proteins
• Senses force transduction
• Can change cell shape & facilitate
movement
• Component of flagella and cilia
• Chromosome organization during cell
division
• Connect directly to cells next door in
tissues
Eukaryotes: some of the other stuff
Centrioles
• Small crystalline polymer tubes made of 9
triplets of microtubules
• Every animal cell has 1 pair
(not in fungi and many groups of plants)
• Arranged as perpendicular pair
(centrosome)
• Starting material for microtubule bundles
used for chromosome organization during
cell division
• Starting point for building flagella and
cilia
Eukaryotes: some of the other stuff
Ribosomes
• BIG proteins
• Protein manufacturing plant
• Produced from the nucleolus
• Found in two places:
• Membrane-bound: RER
Produces most proteins
• Free: Anywhere in the cytosol (but not
the nucleus)
Produces proteins that do not have
cystines (di-cysteine, S-S bridges)
Now for a few words about genomes... How big are they?
 How many genes is a genome?
Organism Genome size* (nucleotide pairs) Approximate Number of Protein-
coding Genes

Homo sapiens (human) 3200 × 10^6 19,000

22,000

Homo sapiens (human) 2800 × 10^6

14,000

Mus musculus (mouse) 180 × 10^6

28,000

Drosophila melanogaster (fruit fly) 103 × 10^6

22,000

Arabidopsis thaliana (plant) 100 × 10^6

6600

Caenorhabditis elegans (roundworm) 12.5 × 10^6

4300

Saccharomyces cerevisiae (yeast) 4.6 × 10^6