Lec 1 Intro Biochem

Introductory Biochemistry
chapter 1
Chemistry is the logic of biological
phenomenon
• Molecules are lifeless. Yet, in appropriate complexity
and number, molecules compose living things.
• These living systems are distinct from the inanimate
world because they have certain extraordinary
properties.
1. They can grow,
2. move,
3. perform the incredible chemistry of metabolism,
4. respond to stimuli from the environment
5. replicate themselves with exceptional fidelity.
• The chemistry of the living cell resembles the chemistry
of organic reactions.
Distinctive Properties of Living Systems
1. The most obvious quality of living organisms is that they are
complicated and highly organized.
• For example, organisms large enough to be seen with the naked
eye are composed of many cells, typically of many types. Inturn,
these cells possess subcellular structures or organelles, which
are complex assemblies of very large polymeric molecules or
macromolecules.
• These macromolecules themselves show an exquisite degree of
organization in their intricate three-dimensional architecture,
even though they are composed of simple sets of chemical
building blocks, such as sugars and amino acids.
• the complex three-dimensional structure of a macromolecule,
known as its conformation, is a consequence of interactions
between the monomeric units according to their individual
chemical properties.
2. Biological structures serve functional purposes.
• That is, biological structures have a role in terms of the organism’s
existence. From parts of organisms, such as limbs and organs, down
to the chemical agents of metabolism, such as enzymes and
metabolic intermediates, a biological purpose can be given for each
component.
3. Living systems are actively engaged in energy transformations.

• The maintenance of the highly organized structure and activity of
living systems depends upon their ability to extract energy from the
environment.
• The ultimate source of energy is the sun. Solar energy flows from
photosynthetic organisms (those organismsable to capture light
energy by the process of photosynthesis) throughfood chains to
herbivores and ultimately to carnivorous predators at the apex of
the food pyramid
4. Living systems have a remarkable capacity for self-
replication.
• Generation after generation, organisms reproduce
virtually identical copies of themselves.
• This self-replication can proceed by a variety of
mechanisms, ranging from simple division in bacteria to
sexual reproduction in plants and animals
• Indeed, if the accuracy of self-replication were
significantly greater, the evolution of organisms would
be hampered.
• This is so because evolution depends upon natural
selection operating on individual organisms that vary
slightly in their fitness for the environment.
Biomolecules: The Molecules of Life
• The elemental composition of living matter differs markedly from the
relative abundance of elements in the earth’s crust.
• Hydrogen, oxygen, carbon and nitrogen constitute more than 99% of
the atoms in the human body with most of the H and O occurring as
H2O.
• Oxygen, silicon, aluminum, and iron are the most abundant atoms in
the earth’s crust, with hydrogen, carbon, and nitrogen being relatively
rare (less than 0.2% each).
• Nitrogen as dinitrogen (N2) is the predominant gas in the atmosphere,
and carbon dioxide (CO2) is present at a level of 0.05%, a small but
critical amount.
• Oxygen is also abundant in the atmosphere and in the oceans.
• H, C, N, and O are among the lightest elements of the periodic table
capable of forming covalent bonds. Two other covalent bond-forming
elements, phosphorus and sulfur, also play important roles in
biomolecules.
• Composition of the Earth’s Crust, Seawater,
and the Human Body*
• See chp 1 for table
Biomolecules Are Carbon Compounds
• All biomolecules contain carbon. The prevalence of C is due to its
unparalleled versatility in forming stable covalent bonds by electron-pair
sharing.
• Carbon can form as many as four such bonds by sharing each of the four
electrons in its outer shell with electrons contributed by other atoms.
• Atoms commonly found in covalent linkage to C are C itself, H, O, and N.
• Hydrogen can form one such bond by contributing its single electron to
formation of an electron pair.
• Oxygen, with two unpaired electrons in its outer shell, can participate in
two covalent bonds, and nitrogen, which has three unshared electrons,
can form three such covalent bonds.
• Furthermore, C, N, and O can share two electron pairs to form double
bonds with one another within biomolecules, a property that enhances
their chemical versatility.
• Carbon and nitrogen can even share three electron pairs to form triple
bonds.
Metabolites and Macromolecules
• The major precursors for the formation of biomolecules are water, carbon dioxide,
and three inorganic nitrogen compounds—ammonium (NH4), nitrate (NO3), and
dinitrogen (N2).
• Metabolic processes assimilate and transform these inorganic precursors through
ever more complex levels of biomolecular order .
• In the first step, precursors are converted to metabolites, simple organic
compounds that are intermediates in cellular energy transformation and in the
biosynthesis of various sets of building blocks: amino acids, sugars, nucleotides,
fatty acids, and glycerol.
• By covalent linkage of these building blocks, the macromolecules are constructed:
proteins, polysaccharides, polynucleotides (DNA and RNA), and lipids.
• (Strictly speaking, lipids contain relatively few building blocks and are therefore
not really polymeric like other macromolecules; however, lipids are important
contributors to higher levels of complexity.)
• Interactions among macromolecules lead to the next level of structural
organization, supramolecular complexes.
• Examples of these supramolecular assemblies are multifunctional enzyme
complexes, ribosomes, chromosomes and cytoskeletal elements.
• Supramolecular complexes have noncovalent forces including hydrogen bonds,
ionic attractions, van derWaals forces, and hydrophobic interactions.
Organelles
• The next higher rung in the hierarchical ladder is occupied by
the organelles,entities of considerable dimensions found only
in eukaryotic cells
• Several kinds, such as mitochondria and chloroplasts, evolved
from bacteria
• Organelles share two attributes,
• 1. they are cellular inclusions usually membrane bounded
2.dedicated to important cellular tasks.
• Organelles include the nucleus, mitochondria, chloroplasts,
endoplasmic reticulum, Golgi apparatus, and vacuoles as well
as other relatively small cellular inclusions, such as
peroxisomes, lysosomes, and chromoplasts.
• The nucleus is the repository of genetic information as
contained within the linear sequences of nucleotides in the
DNA of chromosomes.
Membranes
• Membranes define the boundaries of cells and organelles. They are
• not easily classified as supramolecular assemblies or organelles, although they
share the properties of both.
• Membranes resemble supramolecular complexes in their construction because
they are complexes of proteins and lipids maintained by noncovalent forces.
• Hydrophobic interactions are particularly important in maintaining membrane
structure. Hydrophobic interactions arise because water molecules prefer to
interact with each other rather than with nonpolar substances.
• Hydrophobic interactions are the creative means of membrane formation and
the driving force that presumably established the boundary of the first cell.
• The membranes of organelles, such as nuclei, mitochondria and chloroplasts,
differ from one another, with each having a characteristic protein and lipid
composition suited to the organelle’s function.
• The creation of discrete volumes or compartments within cells is not only an
inevitable consequence of the presence of membranes but usually an essential
condition for proper organellar function.
The Unit of Life Is the Cell
• The cell is characterized as the unit of life, the smallest
entity capable of displaying the attributes associated
uniquely with the living state: growth, metabolism,
stimulus response, and replication.
Biological Macromolecules Are Informational
• Because biological macromolecules have a sense to
their structure, the sequential order of their
component building blocks, when read along the
length of the molecule, has the capacity to specify
information in the same manner that the letters of the
alphabet can form words when arranged in a linear
sequence
Organization and Structure of Cells
• All living cells fall into one of two broad categories—prokaryotic and
eukaryotic.
• The distinction is based on whether or not the cell has a nucleus.
• Prokaryotes are single-celled organisms that lack nuclei and other
organelles;
• The word is derived from pro meaning “prior to” and karyote meaning
“nucleus.”
• In conventional biological classification schemes, prokaryotes are grouped
together as members of the kingdom Monera, represented by bacteria and
cyanobacteria (formerly called blue-green algae).
• The other four living kingdoms are all eukaryotes—the single-celled

Protists, such as amoebae, and all multicellular life forms, including the
Fungi, Plant, and Animal kingdoms.
• Eukaryotic cells have true nuclei and other organelles such as mitochondria
with the prefix eu meaning “true.”
Early Evolution of Cells
• Eukaryotes evolved from the simpler prokaryotes in some
linear progression from simple to complex
• Contemporary evidence favors the view that present-day
organisms are better grouped into three classes or
lineages: eukaryotes and two prokaryotic groups, the
eubacteria and the archaea (formerly designated as
archaebacteria).
• All are believed to have evolved approximately 3.5 billion
years ago from a common ancestral form called the
progenote.
• It is now understood that eukaryotic cells are, in reality,
composite cells derived from various prokaryotic
contributions.
• Structural Organization of Prokaryotic Cells
• Structural Organization of Eukaryotic cells
• See chapter 1 pg 24

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Introductory Biochemistry

3. Living systems are actively engaged in energy transformations.

• The other four living kingdoms are all eukaryotes—the single-celled

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