Questions/Objectives

from last class

I. What is Cell biology and why bother studying
it?
II. What are common features of all living cells?
III. What are features that distinguish major
classes of cells?
IV. How do we believe evolution has contributed
to these similarities and differences?
V. Given the diversity of cells, which types of cells
do cell biologists choose to study???
 Eukaryotes:
III Evolutionarily optimized for complexity and adaptability

e.g. Animal cell

Most morphologically and structurally diverse among the 3 domains:

Can be single-celled or multicellular

Huge range in sizes and shapes (even within a single multicellular organism)

Less diverse in their overall biochemical diversity:

All eukaryotes are really either Organotrophs or Phototrophs
III
Eukaryotes:
Have larger and more complex genomes:
DNA is enclosed within a membranous compartment (nucleus)
Genome is contained within multiple (typically) linear molecules (chromosomes)
Genome size: 12 million 150 billion base pairs
III Notice any trends here?

Table 1-1 (part 2 of 2) Molecular Biology of the Cell, Fifth Edition ( Garland Science 2008)
III A large fraction of gene in eukaryotes code for proteins
that regulate the activities of other genes.

Eukaryotes have often

highly elaborate
gene regulation
schemes.

Figure 1-39 Molecular Biology of the Cell, Fifth Edition ( Garland Science 2008)
III Eukarya and Bacteria: Similarities and Differences

Bacteria Eukarya
Differences Differences
Genetic Machinery
Genetic Machinery Similarities
Cell wall Overall
Overall composition
appearance appearance
Plasma membrane
Reproduction/Cell composition
Reproduction/Cell
Division Division
III Eukarya and Archaea: Similarities and Differences

Archaea Eukarya

Differences
Differences

Overall Similarities Overall

appearance appearance
Genetic Machinery
Reproduction/Cell Reproduction/Cell
Division Division
III Eukaryotes form the third domain of life
6 Kingdoms

Common ancestor

3 domains Common ancestor

 Questions/Objectives
from last class
I. What is Cell biology and why bother studying
it?
II. What are common features of all living cells?
III. What are features that distinguish major
classes of cells?
IV. How do we believe evolution has contributed
to these similarities and differences?
V. Given the diversity of cells, which types of cells
do cell biologists choose to study???
IV

How did Eukaryotic cells arise?

Figure 1-30 Molecular Biology of the Cell, Fifth Edition ( Garland Science 2008)
IV Eukaryotic Cells and the
Endosymbiosis Theory
All eukaryotes have a nucleus (and other internal organelles).
All eukaryotes have mitochondria (take up O2 and harvest energy from
food).
Some eukaryotes have both mitochondria and chloroplasts.

Ancestral eukaryote
(phototroph) Chloroplast
(double membrane)

Engulfing of
photosynthesizing
prokaryote

Engulfing of
an oxygen-
metabolizing
(aka aerobic)
prokaryote
Mitochondrion
(double membrane) Ancestral eukaryote
(organotroph)
 IV Eukaryotic Cells and the
Endosymbiosis Theory
What is some of the evidence for this theory?

Like prokaryotes, both mitochondria and chloroplasts:

are membrane enclosed
have their own genomes in the form of circular DNA molecules
Replicate their own genomes and divide to produce more copies of
themselves
use similar ribosomal complexes for protein synthesis (that are distinct
from eukaryotic ribosomes)
are within the 1 um to 5 um size range
IV
Genetic Change and Evolution
Random change
+
Positive effect on survival
0 Neutral/no effect on survival
- Negative effect on survival
Evolutionary change
Persists in populations
(Frequency increases)
May or may not persist
Evolutionary change
Does not persist
(frequency decreases)
IV Genome Analysis provides a direct means of
deducing evolutionary relationships among species

DNA accumulates random changes through mutation over

long periods of time

The number of nucleotide changes is proportional

evolutionary distance

Some genes evolve rapidly, others are highly conserved

Which types of genes might be highly conserved?

IV More than 200 Gene families are common to all three primary
branches of life. Here are some of them.

Table 1-2 Molecular Biology of the Cell, Fifth Edition ( Garland Science 2008)
IV
The 3 domain classification system came from multi-species
comparisons of nucleotide sequences from a single gene
required for ribosome assembly.
Eukarya
Archaea

Bacteria

A full comparison showed that this gene essentially evolved into 3 branches.
Hence.

Figure 1-21 Molecular Biology of the Cell, Fifth Edition ( Garland Science 2008)
IV No gene is ever entirely new. Innovation can occur in
several ways

Figure 1-23 Molecular Biology of the Cell, Fifth Edition ( Garland Science 2008)
IV Gene Duplication and Divergence is thought to be the
major driving force underlying the appearance of new
genes both within and between species.
Repeated rounds of duplication and divergence over
many millions of years have enabled this gene to give
Primordial Gene rise to a gene family.
Duplication A gene Family

Divergence

Duplication

Divergence

Homologous genes: genes that

share (i.e. derive from) a common
ancestral gene
 When a gene undergoes duplication and divergence
IV within a single organism (or species), it forms
paralogous gene pairs.

Note: Both genes originated

from gene G, and
accumulated changes in
same environment

Figure 1-25b Molecular Biology of the Cell, Fifth Edition ( Garland Science 2008)
 Consider this example: Globin Gene Evolution
IV within Humans

Duplication

Duplication and divergence Duplicated copies end

up getting transposed
to separate
chromosomes

Further duplication
and divergence
IV When a gene diverges after speciation, this divergence
forms orthologous gene pairs.

Both genes originated

from gene G, but
accumulate changes in
separate
environments

Figure 1-25a Molecular Biology of the Cell, Fifth Edition ( Garland Science 2008)
 Consider this example: Globin Gene Evolution across
IV species
Which genes are paralogs?
Which genes are orthologs?
Which genes are homologs?
 Questions/Objectives
from last class
I. What is Cell biology and why bother studying
it?
II. What are common features of all living cells?
III. What are features that distinguish major
classes of cells?
IV. How do we believe evolution has contributed
to these similarities and differences?
V. Given the diversity of cells, which types of cells
do cell biologists choose to study???
V Cell biologists use specific model organisms to
study cellular processes

Model Organism:
Specific species or cell types
Extensively studied in research laboratories
Advance our understanding of
Cellular function
Development
Disease
Research findings can often be applied
toward understanding other organisms / life
in general.
V Most commonly studied Model Eukaryotes

Caenorhabditis elegans
(microscopic worm)
Saccharomyces cerevisiae
(Bakers Yeast)

Danio rerio
(Zebra fish) Mus musculus
Arabidopsis Thaliana (Mouse)
(Plant)
Drosophila Melanogaster
(Fruit fly)

Ideal characteristics of a model organism?

V
Ideal characteristics of model organisms
Are relatively small in size should be able to fit in a cage, petri
dish/test tube, or tank

Are readily available/attainable shouldnt be rare or difficult to

find/catch

Can be easily maintained/propagated in the confines of a laboratory

easy to mate/grow, easy to feed

Have a relatively short life span with discernible developmental

stages and can give rise to a sizeable offspring population

Can be easily manipulated genetically and permit visualization of

resulting phenotypes

Have a genome that has been sequenced.

Check Modules Page for two lecture slides on Model Organisms
 Unit I: What Makes a Cell (Chapters 1-3)
Introduction to Cells / The study of cells
Molecules of Life and Bioenergetics
Physiology in Focus: Metabolic Disorders
Proteins