2. Learning outcomes
Participants should be able to
• Explain what biochemistry means
• Assess the role of biochemistry in nutrition and physiology
• Mention tools for studying biochemistry
• describe the biomolecules
3. Introduction
• Simplest definition: “Chemistry of the living cell”
• Biochemistry happens inside organisms and possibly, the
most obvious thing about living organisms is their
astounding diversity
• The study of the chemical substances and vital processes
occurring in living organisms
• The study of the chemistry behind biological processes
and the synthesis of biologically active molecules are
examples of biochemistry
4. Cont…
• The scientific study of the chemical composition of living
matter and of the chemical processes that go on in living
organisms
• Biochemistry governs all living organisms and living
processes. By controlling information flow through
biochemical signaling and the flow of chemical energy
through metabolism, biochemical processes give rise to
the complexity of life.
5. Introduction…
• Much of biochemistry deals with the structures, functions
and interactions of cellular components such as proteins,
carbohydrates, lipids, nucleic acids and other
biomolecules —although increasingly processes rather
than individual molecules are the main focus.
• Biochemistry studies the chemical properties of important
biological molecules, like proteins, and in particular the
chemistry of enzyme-catalyzed reactions
6. Why study biochemistry
• Lead us to fundamental understanding of life
• Understand important issues in medicine, health, and
nutrition
• Has led to greater molecular understanding of diseases
such as diabetes, sickle cell anemia, and cystic fibrosis.
• Next frontier: AIDS, cancer, Alzheimer’s Disease
•
7. Tools to study biochemistry
• Know the chemical structure and reactivities of
molecules that participate in cellular reactions
• Know the biological function of cellular molecules
• Know how all the pieces and different pathways
fit together
• *use knowledge from general chemistry, organic
chemistry and biology and apply it to biological
systems. Concepts and mechanisms are the same
8. Cont…
Living systems appear complex but there is an
underlying simplicity and elegance;
• Most biological compounds are made up of only
SIX elements; C,H,N,O,P,S
• Only 31 chemical elements occur naturally in
plants and animals
• All organisms have similar biochemical pathways
• All organisms use the same genetic code
• Limited number of molecular building blocks
make up larger molecules
9. Biomolecules
Four major classes of biomolecules serve as
building blocks for larger macromolecules
• Carbohydrates; e.g. glucose, fructose, sucrose
– Mainly used as source off cellular energy
• Lipids; commonly known as fats
– Organic compounds that are not very water
soluble
– Used as source of cellular energy
– Components of cell membrane
10. Cont…
3. Amino acids;
-20 natural amino acids in total
-used as building blocks for proteins
4. Nucleotides
- Five in total
-Used as building blocks for DNA and RNA precursors
11. 5. OTHER
-Vitamins; organic compounds necessary for
proper growth and development
- Heme; organometallic compound containing
iron, important for transporting oxygen in the
blood stream
Building blocks are used to create
macromolecules; polymer of several hundreds
to sometimes millions of building blocks
12.
13.
14. Structure and function of biomolecules
• At a simple level, we can divide molecules up
according to their affinities for water –
hydrophobic (limited solubility in water),
hydrophilic (soluble in water) and amphiphilic
(have characteristics of both hydrophobicity and
hydrophilicity)
• Hydrophobicity in biological molecules arises
largely because carbon-hydrogen bonds have
electrons that are fairly evenly shared (not unlike
carbon-carbon bonds).
15. • By contrast, the electrons between the oxygen
and hydrogen of water are not equally shared.
Oxygen has a greater electronegativity, so it
holds them closer than hydrogen does. As a
consequence, oxygen has what we call a
partial negative charge and hydrogen has a
partial positive charge
16. • Proteins are very large molecules -macro-biopolymers
made from monomers called amino acids.
• There are 20 standard amino acids, each containing a
central carbon atom, a carboxyl group, an amino
group, and a side-chain (known as an "R" group).
• The "R" group is what makes each amino acid different,
and the properties of the side-chains greatly influence
the overall three-dimensional conformation of a
protein.
• When amino acids combine, they form a special bond
called a peptide bond through a condensation reaction,
and become a polypeptide, or protein
17. The Amino acid
• Each amino acid consists of:
– A central carbon atom
– An amino group
– A carboxyl group &
– A side chain
• Differences in side chains distinguish the
various amino acids
19. Cont…
• Though all of the amino acids are, in fact, soluble in water, the
interactions of their side chains with water differ significantly.
This is important, because it is only in the side chains (R-
groups) that amino acids differ from each other
• From the structure above, an amino group has a central
carbon also called a chiral carbon- a carbon atom to which
four different groups are attached. Because of this chirality of
the central carbon atom it can form either L or D amino acids.
L amino acids are the ones incorporated into proteins. Amino
acid chains vary in size, shape and polarity
20. Classification of amino acids
• Side chains of amino acids are responsible for
the many of the unique properties of proteins.
Three major classes of side chains
– Hydrophobic
– Charged
– Polar
– Can also count 4 if Glysine is in own class
21. • The 20 different amino acids are commonly
abbreviated with 1 or 3 letter codes
22.
23. Classification…
• The amino acids can be classified as either hydrophobic or
hydrophilic, depending on the ease with which their side
chains interact with water. In general, proteins fold so that
amino acids with hydrophobic side chains are in the
interior of the molecule where they are protected from
water and those with hydrophilic side chains are on the
surface
• Hydrophilic amino acids have side chains that contain O or
N atoms. Some of the hydrophilic side chains are charged
at physiologic pH. The acidic amino acids (aspartic and
glutamic acids) have carboxyl groups that are negatively
charged, whereas the basic amino acids (lysine, arginine,
and histidine) have nitrogen atoms that are positively
charged
24. Properties of amino acids
• Size and shape
• Charge
• Polarity
• Hydrophobicity
• Aromaticity
• Conformation- usually determined by the side
chain
27. Acid-Base properties of A.A & proteins
• Amino acids and proteins have groups that
can release and bind protons (H+); in other
words, they have acid-base character. The
groups with acid-base character can be
generally represented in one of the two ways
shown below.
28.
29. • The pK value indicates the pH range in which the
dissociation of the H+ occurs. More specifically,
the pK is the pH at which the group is 50%
dissociated, or half of it is in the acid form and
half in the base form. These values of pK are used
in determining the net charge a substance (amino
acid, protein, drug) will have in the body and
which ones will act as good buffers to keep the
pH constant, and to understand pathologic states
of acidosis and alkalosis
30. Classifying acidic & basic amino acids
• Amino acids are classified as acidic or basic according to
their R groups because in proteins, these are the only
groups that can dissociate. The α-amino and α-carboxyl
groups are in peptide bonds and lose their acid-base
character. If an amino acid has a carboxyl in its R group,
that amino acid is said to be acidic because the carboxyl
dissociates in the acidic (pH <7) range of the pH scale.
Therefore, aspartic acid (pK.4) and glutamic acid (pk 4) are
acidic amino acids. At physiologic pH:
• Their R groups are completely dissociated.
• They carry a charge, e.g., are ionized.
• They contribute negative charge to proteins that contain
them
31. Cont…
• If an amino acid has an amino group as part of
the R structure, that amino acid is said to be basic
because the amino group dissociates in the basic
(pH> 7) range of the pH scale. Therefore lysine
(pK 10) and arginine (pK 13) are basic amino
acids. At physiologic pH:
• Their R groups are completely undissociated.
• They carry a charge, e.g., are ionized.
• They contribute positive charge to proteins that
contain them
34. Optical Activity
• All amino acids except glycine are optically
active and rotate polarized light. Optically
active molecules have a symmetry such that
mirror images are not superimposable
