Biochemistry

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Introduction to
Basic Biology
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What is Biochemistry?

▪ Biochemistry is the branch of science that

explores the chemical processes within and
related to living organisms. It is a laboratory-
based science that combines biology and
chemistry.
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The Bio in Biochemistry

▪ Biology is the scientific study of life and

living organisms, encompassing their
structure, function, growth, evolution,
distribution, and taxonomy.
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▪ The most obvious thing about

living organisms is their
astounding diversity. Estimates
put the number of eukaryotic
species at about 8.7 million, while
bacteria account for one trillion
different species. The number of
species of archaea is still
uncertain, but is expected to be
very large.
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▪ These organisms, representing the three

great domains of life, together occupy every
environmental niche imaginable, from the
human gut to the frozen expanses of the
Antarctic.
▪ Some organisms, like the tardigrades or
water bears, can withstand incredibly harsh
conditions from a few degrees above
absolute zero to 300°F, the vacuum of outer
space, and pressures greater than those at
the greatest depths of the ocean.
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▪ Despite the differing demands of existence in

these widely varied environments, all living
things share some common characteristics.

▪ The most noticeable of these is that from

hummingbirds to humpback whales, from
fungi to frogs, and from bacteria to birch trees,
all living things are made up of cells.
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▪ This fact was first discovered
by Robert Hooke, in 1665,
when he used a microscope to
look at a slice of cork and found
that it seemed to be made up of
tiny chambers that he named
cells.
▪ Subsequent examination of
other living things revealed that
they, too, were, without
exception, made up of cells.
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▪ Today, we know that organisms in all three domains of

life – bacteria, archaea and eukaryotes, share this
property – they are all made up of cells.
▪ For some, a single cell is the organism, while others
are multicellular, like humans, wombats or weeping
willows.
▪ The special characteristics of cells influence the unique
chemistry of life. It is, thus fitting, to take a quick look
at cells, the setting in which the molecular events of
life take place.
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Cell
▪ The cell is the basic unit of life. It is the
fundamental structural and functional unit of all
living organisms. It is often called the building block
of life.
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▪ All cells, no matter what kind, have a plasma

membrane that serves as a boundary for the cell,
separating it from its surroundings.
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▪ They also possess a genome made up of
DNA that encodes the information for
making the proteins required by the cell.

▪ To translate the information in the DNA

and make the proteins it encodes, all
cells have the machinery for protein
synthesis, namely, ribosomes and
tRNAs.

▪ DNA is also the repository of information

that gets copied and transmitted to the
next generation, allowing living cells to
reproduce.
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▪ All cells also need to be able to obtain
and use energy. The source of this
energy is different in different
organisms. Phototrophs are organisms
Plants
that obtain metabolic energy from light,
while chemotrophs get their energy
from the oxidation of chemical fuels.
Organisms that can capture energy
from light or from chemical sources are
termed autotrophs (auto=self,
troph=nourishing). Nitrosomonas sp.
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▪ Others are heterotrophs, which use, as their energy source, the
organic compounds made by other organisms. Plants, and
other photosynthetic organisms are autotrophs, while animals
are heterotrophs.
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▪ Cells may be aerobic (i.e.,
use oxygen) or anaerobic
(able to live without oxygen). Mycobacterium tuberculosis
Some anaerobic cells are
obligate anaerobes, that is,
they require an environment
free of oxygen. Others are Clostridium perfringens

facultative anaerobes, cells

that can live with, or without,
oxygen.
Escherichia coli
 Prokaryotic vs. Eukaryotic cells
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▪ Organisms may be divided into two major groups, the prokaryotes and
the eukaryotes. The cells of the former lack a nucleus and other
organelles, while those of the latter are characterized by numerous
internal, membrane-bounded compartments, including a nucleus.
Prokaryotic
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▪ Prokaryotes are unicellular and generally
considerably smaller than their eukaryotic
cousins, with sizes ranging from 0.5 to 5 μm
in diameter.

▪ Prokaryotes typically have circular

chromosomes, and may sometimes contain
extra-chromosomal DNA elements (also
usually circular) called plasmids.

▪ Although the DNA in prokaryotes is not

wrapped around histones, as is the case for
eukaryotes, prokaryotes have proteins
associated with their DNA.
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Prokaryotic cells
▪ The DNA-protein complexes in
prokaryotes create a structure called a
nucleoid, which is different from the
eukaryotic nucleus in not being enclosed
by a nuclear envelope. The proteins
associated with the DNA in Archaea
resemble eukaryotic histones, while those
in bacteria are different from both
eukaryotic and archaeal DNA packaging
proteins.
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▪ Prokaryotes may be divided into two broad categories,

bacteria and archaea. These single-celled organisms are
both ancient and widespread. Archaea were once thought
to be a subgroup of bacteria, but have subsequently been
shown to be a completely different group of organisms that
are so distinct from both bacteria and eukaryotes that they
now are classified in a domain of their own.
 Bacteria
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▪ Like eukaryotic cells, bacterial cells have a

plasma membrane surrounding them, but in
addition, they also contain an exterior cell wall,
comprised of an interlocked peptidoglycan
network.

▪ On their exterior surfaces, bacteria have hair-like

appendages called pili that allow them to adhere
to other cells. Pili play an important role in
bacterial conjugation, a process in which DNA is
transferred between bacterial cells. Escherichia coli

▪ In addition, bacterial cells may have flagella that

enable them to move through their surroundings.
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▪ Interestingly, bacteria can communicate, not only

with members of their own species, but also with
other bacterial species, using chemical signals, in
a process called quorum sensing.

▪ These signaling mechanisms enable bacteria to

assess conditions around them (such as the size
of their population). Quorum sensing plays a
role in the process of infection by bacterial Quorum sensing | Cell communication
pathogens as well as the formation of biofilms | Bacteteria | virulence | AHL | Ligand |
Basic Science Series (youtube.com)
(mats of cells that adhere to each other tightly
and protect the bacteria against environmental
hazards or other harmful agents).
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Archaea

The first archaeans to be studied were all

found in harsh environments such as salt flats
and hot springs. Because of this, they were
initially believed to live only in extreme
environments and were described as
extremophiles. We now know that archaeans
can be found in every environment, moderate
or extreme. Archaea have been found in the
human gut, and in such huge numbers in
marine plankton that it has been suggested
that they may be the most abundant
organisms on earth.
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▪ While they are unicellular, and
superficially resemble bacteria,
archaea are in some respects more
similar to eukaryotes.

▪ Their transcriptional machinery,

promoter sequences and ribosomes
are much more like those of eukaryotes
than of prokaryotes.

▪ Archaea are also unique among living

organisms in their use of ether linkages
to join the lipids used in their plasma
membranes to glycerol.
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▪ Not only are the ether linkages different
from the ester linkages in all other
forms of life, but the lipids themselves
are different.

▪ In place of the fatty acids used in both

bacterial and eukaryotic membranes,
archaea use long isoprene-derived
chains.

▪ This difference in membrane

composition and structure makes
archaeal membranes highly stable and
may be advantageous in extreme
conditions.
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▪ Archaea, like bacteria, also have a cell wall,

but the cell walls do not contain
peptidoglycans. Some archaea have
peptidoglycan-like molecules in their cell
walls, while others build their cell walls
entirely of glycoproteins and
polysaccharides.
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 Eukaryotes
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▪ Eukaryotic cells are found in both unicellular and

multicellular organizational schemes. Unicellular forms
include yeast and many protists, familiar to students
from introductory biology labs, like Paramecium and
Amoeba.

▪ Multicellular eukaryotes include plants, animals, and

fungi. Eukaryotic cells are surrounded by a plasma
membrane. Animal cells have no cell walls, whereas
plant cells use cellulose, hemicellulose, and pectins to
build cell walls outside their plasma membranes.

▪ Fungal cells have cell walls that are unusual in

containing the polymer, chitin, which is also found in
the exoskeletons of arthropods.
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▪ Eukaryotic cells are typically much larger (typically

10-100 μm) and contain considerably more DNA
than prokaryotic cells. The most distinctive feature
of eukaryotic cells, however, is the presence of a
variety of internal membrane-bounded structures,
called organelles.