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Introduction to Molecular
Biology
BIOS 302
Northern Illinois University
What is Life?
• NASA definition: “Life is a chemical system capable of Darwinian
evolution”.
• The two fundamental principles of life:
1. Life is a complex set of chemical reactions, but there is no fundamental
difference between living and non-living material. No “vital principle” that
separates life from non-life.
• Also implies that studying how living things work means studying the chemical reactions
involved.
2. Life evolves through natural selection. Over time, living things become
more capable of surviving and reproducing by the process of random
mutations followed by interactions with their environment and each other.
• By examining a wide range of species we can learn about what mutations have proved
useful.
The Chemical Reactions
of Life
• To survive, a cell must do many things:
• Homeostasis: maintain a relatively constant
internal state different from the outside: pH, ion
concentrations, temperature, macromolecule
concentrations
• Metabolism: take in energy and materials from
the outside and convert them into compounds
that become part of the organism
• Respond to environment to optimize its situation:
adapt to external conditions to acquire food and
avoid harmful things
• Growth and Reproduction: make more copies of
itself, passing genetic information to offspring.
To accomplish these things:
• Separation of living material inside from non-living
outside: a cell membrane, composed of lipids. The
membrane is hydrophilic (water-loving) on its faces,
but hydrophobic on the inside. This creates a barrier
that very few molecules can go through without help.
• Bring in raw materials and energy from the outside.
Raw materials pass through the membrane through
protein channels.
• Utilize many chemical reactions to convert the raw
materials into parts of the organism.
• Each reaction needs a separate catalyst: enzymes. Most
enzymes are proteins.
• Store and transmit information on how to build the
necessary proteins: DNA and the processes of gene
expression.
Membrane
Transport
• It takes a lot of different proteins
to do all the specific processes in
a cell. The human genome
contains about 25,000 genes. At
least 1550 are known to be
membrane transporters.
• Another very large group of
membrane proteins are
receptors, which detect specific
compounds outside the cell and
pass that information into the
cell.
• About 25% of the human
genome is devoted to membrane
receptors and transporters.
• Just to get a feel for how many proteins
are needed for membrane transport,
here is a diagram of various types of
transporter, using different mechanisms
to move some specific compound across
the membrane.
• This diagram is a partial list
of the specific transporters
needed to move things
across the mitochondrial
membrane.
• Converting compounds from the outside world
(food) into parts of the living cell. This requires
many reactions, and each reaction is catalyzed by its
own specific enzyme.
A small part of the metabolic activities in a cell. Glycolysis is the
breaking down of glucose into pyruvate. This generates energy
(in the form of ATP) . Also, pyruvate is the raw material for
several other necessary compounds in the cell.
Metabolic Activities
A chart of the main metabolic
reactions in human cells. The
image needs to be blown up
much larger to be readable.
There are thousands of reactions
shown here.
Proteins and DNA
• It is clear that the cell needs thousand of
different proteins.
• Proteins are composed of linear chains of amino
acids. There are 20 amino acids in common use.
• The type of amino acids and their order in the protein
chain determines the folding pattern and the function
of the protein.
• The 3-dimensional structure of each protein is unique.
• Proteins can’t reproduce themselves.
• The cell makes the proteins it need by storing
information about the amino acid sequence of
each protein in its DNA, then using that
information to synthesize the proteins.
• DNA is a much more regular and simple a
molecule than proteins are. All DNA,
regardless of what proteins it codes for, is
a double helix composed of strands of
nucleotide , which contain 4 types of
nucleotide.
• The simple structure makes DNA easy to
replicate, easy to work with during the
process of gene expression, and stable for
long term storage.
• This simple, regular structure also makes DNA
easy to manipulate and sequence in the
laboratory.
• Especially important: if you know the DNA
sequence that codes for a protein, you can
instantly deduce its amino acid sequence (the
genetic code).
DNA
Gene Expression
• The proteins a cell needs are made by the process of gene expression
• Gene expression is a 2 step process:
• First, the region of DNA that is the gene is copied into RNA. This process
is transcription.
• Then, information in RNA is converted into the amino acid sequence of
proteins (translation)
• Also important: to reproduce, the cell must make new copies of its
DNA. This is the process of replication.
• These three processes, replication, transcription, and translation,
define the flow of information in the cell. Together, they are called
the Central Dogma of Molecular Biology.
• A corollary: Information does not flow from protein back to DNA. This is
a molecular version of the incorrectness of “inheritance of acquired
characteristics”. Changes in proteins do not affect the DNA in a
systematic manner (although they can cause random changes in DNA).
• This class deals with the molecules of the Central Dogma (DNA, RNA,
protein), the processes of replication, transcription and translation
(plus supporting processes), and the control of these activities.
Evolution
Evolution
• “Nothing in biology makes
sense except in the light of
evolution.”
• The basic principle of
evolution by natural
selection: mutations occur
randomly, and those
mutations that increase
evolutionary fitness (the
ability to survive and
reproduce) tend to spread,
because individuals with
those mutations
outcompete others and
end up with more
descendants.
Mutations
• A mutation is any change in the DNA nucleotide sequence.
• Some changes are very small: one nucleotide substituted for another.
• Other changes are very large: chromosome rearrangements and whole genome duplications,
for instance.
• Mutations can alter the structure of proteins, as well as the time, place, and
amount at which they are produced.
• We will study various types of mutation: how they arise and what their effects
are.
Brief History of Life on Earth
• The Universe begins as an incredibly hot dense point that explodes outward: the Big Bang,
13.8 billion years ago
• The Earth, the Sun and the rest of our Solar System form from a cloud of gas and dust: 4.6
billion years ago
• A period of bombardment by large objects from space keeps Earth’s surface molten for
several hundred million years. During this time, many organic molecules are formed:
prebiotic chemistry
• First evidence of life on Earth is form about 3-3.5 billion years ago. Life has been on Earth
through most of its history.
• Cyanobacteria evolve a form of photosynthesis that generated oxygen as a waste product.
The resulting oxygen poisons many organisms, but allows much more efficient energy
production. About 2.5 billion years ago.
• Eukaryotes appear, with mitochondria that can use the oxygen, and a much greater diversity
of forms than found in prokaryotes, about 1 billion years ago.
• Multicellular organisms, with all of today’s major phyla, appear about 600 million years ago
(the Cambrian explosion).
• Two major mass extinction events: Permian (200 million years ago) and Cretaceous (65
million years ago), plus many smaller mass extinctions, alter the number and distribution of
living forms.
Prebiotic Chemistry
• The evolution of the organisms we see today occurred
over a very long time. Here we see a quick look at the
origin of life and how things have changed over time.
• The main elements in living things: carbon, hydrogen,
oxygen, and nitrogen, are among the most common
elements in the Universe.
• Hydrogen has been here from the beginning. The other
elements were formed as part of nuclear fusion in stars.
• Many simple organic (carbon-containing) compounds
have been detected in outer space, either in
meteorites or by the patterns of electromagnetic
radiation they absorb and emit.
• Heat, pressure, lightning, UV light, and other energy
sources created more such compounds (and more
complex compounds) in the atmosphere and oceans of
the primitive Earth.
Origin of Life
• There is no scientific consensus about how life began—not even a solid
theory, just a number of hypotheses without compelling evidence.
• Primordial soup. Organic compounds, including many found in living organisms,
can be formed from gases that existed on the primitive Earth by lightning, radiation,
or heat. They also are found in comets: organic compounds are very common in
outer space as well as on Earth. They were undoubtedly present from the beginning
on Earth.
• Darwin’s idea, still reasonable today: life may have begun in a "warm little pond,
with all sorts of ammonia and phosphoric salts, lights, heat, electricity, etc.
present, so that a protein compound was chemically formed ready to undergo
still more complex changes….At the present day such matter would be instantly
devoured or absorbed, which would not have been the case before living
creatures were formed.“
• Deep sea vents (iron-sulfur world). Lots of chemicals that can be used to
generate energy, catalysis maybe occurred on iron-sulfur crystals. The idea
here is that maybe life started under harsh conditions: high temperatures
and pressures, and not in a nice warm little pond.
• Lots of other theories.
RNA World Hypothesis
• RNA molecules are capable of both storing information and catalyzing
chemical reactions. In present day cells, DNA stores information and
proteins perform catalysis, with RNA as the intermediate between DNA
and protein.
• One can imagine a time when there was no DNA or protein, just RNA
performing both information storage and catalysis: this is the RNA
World hypothesis.
• Very long ago, at least 3.5-4 billion years ago. (Recall the Earth is 4.6
billion years old, and didn’t have a stable solid surface until about 4
billion years ago).
• Presumably there was once a self-replicating RNA molecule. However,
no such RNA has been found or made artificially so far.
• The RNA World hypothesis is an intriguing concept, but there is very
little real evidence for it. But during this course we will occasionally
note the central role played by RNA in basic cellular processes.
All Cells Have Evolved from a Common Ancestor
• We strongly believe all cells all descended
from a single primitive organism, the Last
Universal Common Ancestor (LUCA).
• Probably 3-3.5 billion years ago or so.
• Long after the end of the RNA World (if it ever
existed)
• The LUCA was not the first living cell. It was
the cell whose descendants eventually
outcompeted all other cells. Lots of other
cells and forms of life undoubtedly existed
then, but eventually became extinct.
• No one has ever found an organism that
didn’t fit this model.
All Cells Use the Same Basic Chemistry
• The main reason we think there was a
common ancestor of all living things.
• Same macromolecules: proteins,
nucleic acids, carbohydrates, and lipids
• Same subunits and functions for these
macromolecules:
• All cells store their information as DNA,
using the same 4 nucleotides.
• All cells use RNA as an intermediate
between DNA and protein, using the same
genetic code to translate the sequence of
bases into amino acids.
• All cells use proteins to do most of the
work of the cell, and the proteins all use
the same 20 amino acid subunits.
Prokaryotes and Eukaryotes
• The defining difference between prokaryote and eukaryote
is that eukaryotes have their DNA stored in a membranebound nucleus, while prokaryotes have their DNA floating
freely in the cytoplasm.
• Prokaryotes are single celled organisms that are simpler
than eukaryotes. They are also far more diverse in the
conditions they grow in and their biochemistry.
• Prokaryotes have a single circular chromosome, and very few if any
internal membranes or membrane-bound organelles. Transcription
of the DNA into RNA and translation of RNA into protein occur
simultaneously in a single location.
• All large multicellular organisms are eukaryotes: plants,
animals, fungi, seaweed, etc. There are also a large and
diverse group of single celled eukaryotes (protists).
• Eukaryotes have multiple linear chromosomes, internal membranes,
and transcription occurs in a separate location from translation.
• Much of this course (and BIOS 303) is devoted to eukaryotic
biology, but I will try to bring in some prokaryotic things when
appropriate.
Tree of Life
• Evolutionary descent is traced through differences in
genes: the more mutational differences that have
accumulated between two species, the further back in
time their common ancestor lived.
Carl Woese, discoverer of
the Archaea and the use of
16S RNA in phylogeny
• One of the very few genes found in all organisms is the
gene for 16S ribosomal RNA.
• It is an essential component of the protein synthesis
machinery.
• Called 18S RNA in eukaryotes
• By tracing the accumulation of mutational changes, it is
possible to generate a single tree showing the descent of
all organisms from a common ancestor.
• Biggest surprise: the prokaryotes are divided into 2 very
different groups: the Bacteria and the Archaea.
• Note how small the branches are for plants, animals and
fungi: the organisms we can see are only a tiny part of
the diversity of life.
• We will look into how changes in DNA have been used to
trace the relationships between different species.
Three Domains of life:
Bacteria, Archaea, and
Eukarya
Cell Basics
The Cell Theory
1. All living organisms are composed of cells.
• Note that there are areas in the body that are outside of
cells, however
2. The cell is the basic unit of life.
• It is the minimum level of complexity that displays all the
characteristics of life
3. All cells originate from previously existing cells.
The first person to see
microorganisms, Anton van
Leeuwenhoek, used a powerful
(250x) single lens.
• Origin of life problem
• This theory has been around since the 1830’s. It is
well accepted in the scientific community because
there has been a lack of any good counterexamples.
• Based on microscopic examination of plants,
animals, and other organisms.
Robert Hooke invented the
compound microscope (using
2 lenses): 1665
Cells are Very Diverse
(A) Ner e cell in the cerebellum
(B) Paramecium (single celled
eukaryote)
(C) Section of a plant stem
(D) Bacterium (Bdellovibrio
bacteriovorus)
(E) Macrophage (white blood cell)
engulfing a red blood cell
Unicellular vs. Multicellular
• Organisms can be unicellular or multicellular.
• Multicellular organisms have many cells,
which are differentiated into different cell
types, with different functions.
• Within the bodies of multicellular organisms
there are spaces outside of the cells: the
extracellular matrix.
• Unicellular organisms perform all the
activities of life within a single cell.
• There are also colonial organisms, where all
the cells have identical (or almost identical)
functions, but they are joined together into a
unit.
Components of Cells
• All cells are surrounded by a cell membrane
that allows very few things other than water to
get in or out without regulation.
• All cells contain DNA, which has the
instructions to run the cell as well as reproduce
it.
• All cells contain cytosol, an aqueous semiliquid containing all the chemicals needed to
maintain life.
• Cytosol is sometimes called cytoplasm, which
implies that it is outside the nucleus.
• All cells take in food—both materials and an
energy source, and convert it to parts of the
cell itself. Waste heat and materials are then
excreted from the cell.
• All cells respond to the environment, seeking
out opportunities to live, grow, and reproduce;
and avoiding/defending against things that will
hurt it.
Major themes/concepts in 302
• Molecular biology focusses on storage, expression , and transmission of genetic
information: DNA, RNA, protein.
• What are the molecules that drive life?
• How do shape and structure of molecules relate to function?
• How do molecules influence/regulate biological pathways? (Gene expression and
regulation)
• How do we study molecules?