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Chapter
1
Biochemistry
Benjamin R. Canida, D.D.S.,
Kyle M. Cheatham, O.D., F.A.A.O.,
Kendra Dalton, O.D.
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CHAPTER 1. BIOCHEMISTRY
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SECTION 1.1
The Cell
Eukaryotic cells are composed of multiple internal membranes that form organelles. Organelles are living compartments inside the cell that serve a particular role in maintaining the health and function of the cell. Certain biochemical
processes necessary for cell survival cannot occur in the regular internal environment of the cell due to denaturation of proteins or competition between various enzymes. The compartmentalization of biochemical processes within
specific organelles ensures an appropriate environment that will allow these
processes to function properly.
Cell structure
We will now provide a brief review of cell structure and the function of organelles. Please refer to the histology chapter for more details regarding the
cell.
The cell is separated from the external environment by the plasma membrane composed of phospholipids, proteins, and carbohydrates. The
plasma membrane plays a role in the following functions:
• Cell-cell adhesion
• Cell protection
• Cell communication
The environment outside the plasma membrane is termed the extracellular
environment. The intracellular environment is composed of fluid (the
cytosol) and solid living compartments (the organelles).
• Glycolysis, the first step in the breakdown of carbohydrates into
ATP, occurs within the cytosol.
Cell organelles include the following:
• The nucleus contains DNA in the form of chromosomes which serve
as the genetic blueprint of the cell. DNA replication, mRNA
transcription, and tRNA transcription occur in the nucleus.
– The nucleolus is a region within the nucleus that contains
dense chromatin and serves as the site for rRNA transcription.
• Ribosomes are non-membrane bound structures that are essential
for translation of mRNA into proteins.
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1.1. THE CELL
• The rough endoplasmic reticulum surrounds and is connected
to the perinuclear space of the nucleus and is bound to multiple ribosomes. It is involved with the production of extracellular proteins.
• The smooth endoplasmic reticulum is continuous with the rER
and does NOT contain ribosomes. Functions of the sER include:
– Steroid production in the adrenal cortex.
– Storage and breakdown of glycogen and detoxification of lipid
soluble drugs.
– Storage and release of calcium for muscle contractions in muscle
cells.
• The Golgi apparatus helps the rER modify proteins that will be
exported into the extracellular environment.
• Lysosomes contain multiple enzymes responsible for digestion of
waste components within the cell.
• Mitochondria are termed the “powerhouse” of the cell as it serves
as the location for the Krebs cycle and oxidative phosphorylation, processes necessary for the production of ATP.
Proteins contain specific sequences that serve as a marker for the
final destination of the protein within organelles, the cell cytosol,
or the extracellular matrix.
Cell communication
Cell-cell communication is essential for cell survival and plays a role in the
regulation of cell metabolism, proliferation, differentiation, and cell movement.
Cell communication includes direct cell-cell signaling or the release of signal
molecules that act on local or distant target cells.
Direct cell-cell signaling plays an important role in the embryonic development and differentiation of cells, cellular proliferation, and cell survival. Direct
cell-cell signaling involves the following modes of communication:
• Gap junctions connect the cytoplasm of adjacent cells and serve as a
passageway for small hydrophilic molecules, ions, and metabolites to pass
directly from one cell to another.
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CHAPTER 1. BIOCHEMISTRY
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Gap junctions are often found in abundance in tissues such as the
heart that require a synchronous and rapid response of multiple
cells to electrical or other types of signals. Gap junctions are also
crucial for the nourishment and survival of cells that are located
far away from blood vessels, including the intraocular lens.
• Cell surface adhesion molecules such as integrins and cadherins also
serve as signal molecules that bind to surface receptors on adjacent cells
to help regulate cell proliferation, cell differentiation, and maintain the
proper internal cellular environment.
Cell signaling through the secretion of signaling molecules can be divided
into three modes of communication:
• Endocrine signaling involves the release of hormones that are
carried to distant target cells through the bloodstream.
– A variety of hormones are secreted from endocrine glands including the gonads, the pituitary, thyroid, pancreas, and adrenal
glands (see general physiology chapter for further details).
• Paracrine signaling occurs when a signal molecule released from
one cell acts on a local neighboring cell.
– The release of neurotransmitters into the synapse between
neighboring neurons is an example of paracrine signaling.
• Autocrine signaling occurs when a cell responds to its own signal molecule that it released.
– T-lymphocytes often produce a growth factor that initiates their
own proliferation in response to a foreign antigen.
Signal transduction
Cell communication through the release of signal molecules involves the initiation of signal transduction cascades within the cell, resulting in the activation of certain enzymes and transcription factors that alter gene expression
within the cell nucleus.
• When a signal molecule (aka ligand) binds to a transmembrane protein
receptor, the ligand produces a conformational change in the protein that
is then detected in the cytoplasm.
• Many protein receptors are coupled to GTP, forming a G protein. The
conformational change in a G protein often leads to the activation of
adenylyl cyclase, an enzyme that produces multiple secondary messengers
known as cAMP molecules.
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1.1. THE CELL
• Although cAMP molecules may act on a variety of molecules within the
cell, it often activates protein kinase A, an enzyme responsible for the
phosphorylation of multiple target proteins that produce a widespread
effect on cellular biochemical processes, including gene expression.
– Polypeptide hormones, such as glucagon, epinephrine, and parathyroid hormone, activate adenylyl cyclase.
– Insulin leads to the activation of tyrosine kinase.
• Additional signal transduction pathways include cGMP, PIP2 transmembrane proteins, MAP kinsases, and Ras proteins.
Signal transduction cascades result in signal amplification. A
single ligand that binds to a transmembrane protein receptor results in the production of multiple secondary messengers that then
act on an even greater number of target enzymes, producing a
widespread effect throughout the cell.
Chemical bonds
There are a variety of chemical bonds that are important for maintaining the
structure of carbohydrates, proteins, lipids, and nucleic acids, the main components of cell structure and biochemical processes.
• Covalent bonds involve the sharing of electrons between two molecules
and are the strongest of all the chemical bonds.
• Non-covalent bonds (those that do not involve a sharing of electrons)
include:
– Electrostatic interactions occur between negatively and positively charged atoms.
– Hydrogen bonds are relatively weak bonds that form between
two electronegative atoms that share an H atom (H2 O is the classic
example).
– Van der Waals interactions are momentary bonds between two
oppositely charged atoms. Van der Waals interactions between two
molecules constantly change as the electric charge around the atom
changes over time.
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SECTION 1.2
Proteins
Protein Structure
We now summarize concepts regarding proteins. Proteins are comprised of
amino acids linked covalently by peptide bonds.
Amino acids (AAs) are comprised of an amino group (N H2 ), a carboxyl
group (COOH), a hydrogen atom (H), and a functional group (R) attached to
a central carbon atom (C).
• Each amino acid has a unique functional group (R) that differentiates
proteins from one another.
There are 20 amino acids that can be classified in several different ways:
1. Essential vs nonessential AAs.
• There are 11 nonessential amino acids that the body is able to
synthesize from glucose:
– Arginine
– Aspartate
– Asparagine
– Alanine
– Cysteine
– Glycine
– Glutamate
– Glutamine
– Proline
– Serine
– Tyrosine
Amino Acid (AA)
R
COOH
C
NH2
Figure 1.1:
H
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1.2. PROTEINS
• The other 9 amino acids must be consumed through the diet
(essential AAs):
– Phenylalanine
– Valine
– Threonine
– Tryptophan
– Isoleucine
– Methionine
– Histidine
– Lysine
– Leucine
• Although arginine, cysteine, glutamine, and tyrosine are
commonly considered nonessential AAs, they may become essential under conditions of stress or illness (i.e. conditionally
essential or semiessential AAs).
– Tyrosine is synthesized from the essential AA phenylalanine.
Patients with phenylketonuria (PKU) lack the necessary enzyme to metabolize phenylalanine to tyrosine. Because tyrosine can no longer be produced, cells are now dependent
on obtaining this AA from the diet.
2. R-Group
3. Polar (12 AAs) vs nonpolar (8 AAs)
4. Acidic, basic, or neutral
5. Metabolic end product
• Ketogenic - yields Acetyl CoA
– Leucine, Lysine
• Glucogenic - yields pyruvate
– Arginine, Aspartate, Asparagine, Alanine, Cysteine, Histidine, Methionine, Glycine, Glutamate, Glutamine, Proline,
Serine, Threonine, Valine
• Both Ketogenic and Glucogenic
– Isoleucine, Phenylalanine, Tryptophan, Tyrosine
Multiple amino acids are linked together by a peptide bond (i.e. amide
bond), a covalent bond between the N H2 group of one amino acid and
the COOH group of a fellow amino acid. The formation of a peptide
bond releases H2 O.
• Dipeptide: 2 AAs bound together.
• Tripeptide: 3 AAs bound together.
• Polypeptide: 4 or more AAs bound together.
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The lengths of polypeptides can vary greatly. When the length
of polypeptides becomes very large (involving > 100 AAs), the
structure is termed a protein.
Amino acids have several functions within the body:
• Serve as the building blocks of proteins.
• Serve as substrates for the production of metabolic energy.
• Serve as precursors for the synthesis of heme, coenzymes, melanin,
collagen, etc.
–
–
–
–
–
–
–
–
Glycine is a precursor of porphyrins such as heme.
Arginine is a precursor of nitric oxide.
Tryptophan is a precursor for serotonin (a neurotransmitter).
Tyrosine (derived from phenylalanine) is a precursor for dopamine,
epinephrine, and norepinephrine (catecholamine neurotransmitters).
Glycine, glutamine, and aspartate are precursors for nucleotide
synthesis.
Glutamate is a precursor of the neurotransmitter GABA. Glutamate is converted to GABA via the enzyme L-glutamic acid
decarboxylase using pyridoxal phosphate (the active form of
vitamin B6) as a cofactor.
Phenylalanine is a precursor of phenylpropanoids (aid in plant
metabolism).
Histidine is transformed into histamine via histidine decarboxylase. Recall that histamine is a vasodilator released by mast
cells and basophils.
Albinism is a group of genetic disorders characterized by mutations in the enzyme tyrosinase, which is necessary for the conversion
of tyrosine to melanin.
Structural levels of proteins
Proteins have four distinct structural levels:
1. Primary: Amino acid sequence of the protein. Each protein has a
different primary structure.
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1.2. PROTEINS
2. Secondary: Refers to local interactions between neighboring amino
acids that cause twisting within the protein helix that is stabilized by
hydrogen bonds. Examples of common secondary structures include:
• Alpha helices: Most common in transmembrane proteins and insoluble proteins.
• Beta sheets: Commonly found in soluble proteins. Beta turns
connect beta sheets.
• Random coils: Connect different secondary structures together.
3. Tertiary: A polypeptide chain bends and folds on itself, creating a three
dimensional protein shape that is often stabilized by covalent disulfide
bonds. Common tertiary structures include:
• Globular structure: Water soluble polypeptide chains that fold
tightly on themselves to create a compact, spherical shape. Plasma
proteins (e.g. albumin), transport proteins, nuclear proteins, and
most enzymes have a globular tertiary structure.
• Fibrous structure: Water IN-soluble polypeptide chains that extend along one axis. These proteins are most often involved in protection and maintaining cell/tissue structure and include collagen,
keratin, and elastin.
4. Quaternary: Multiple polypeptide chains linked together with noncovalent and covalent disulfide bonds to form multimers. Examples
include hemoglobin (4 polypeptide chains) and insulin (2 polypeptide
chains).
Physiologically relevant proteins
Enzymes: Proteins that serve as catalysts by lowering the activation energy needed to initiate a reaction. Each enzyme has a unique active site that
is specific for a particular substrate.
Antibodies: Highly specific Y-shaped proteins produced by plasma cells in
response to an antigen. These proteins function in the immune response.
Antibodies are either secreted into the systemic circulation or they act as antigen receptors on the surface of B-cells.
IgM: First antibody made in response to an antigen. Found primarily in the
blood and on the surface of immature B-cells.
IgG: Most plentiful Ab in circulation. IgG is the only Ab that is able to cross
the placenta to protect the fetus. IgG provides the majority of Ab-based
protection against antigens.
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IgA: Primary antibody in excretions such as mucous, saliva, tears, and breast
milk.
IgD: Acts as an antigen receptor on the surface of mature B-cells.
IgE: Binds to allergens and triggers histamine release from mast cells, leading
to allergy symptoms and type 1 hypersensitivity reactions. IgE also
provides protection against parasites.
Collagen: Fibrous protein that provides tensile strength to tissues including
tendons, ligaments, skin, muscles, blood vessels, bone and teeth. Collagen is
the most abundant protein in the body, accounting for 25-35% of the body’s
total protein content.
• Procollagen, produced in the rough ER, is the initial precursor to collagen and consists of 3 polypeptide strands stabilized by disulfide bonds
and eventually wound into a triple helix. Each polypeptide strand consists of Glycine-X-Y repeats (proline and lysine are commonly in the X
and Y positions).
• The first essential step in the post-translational modification of procollagen to tropocollagen (occurs in the Golgi appartus) involves the hydroxylation of lysine and proline residues within the polypeptide strands.
Vitamin C is an essential cofactor for the hydroxylase enzymes that
are responsible for these modifications.
• Procollagen is further modified into tropocollagen by removing the terminal ends of the polypeptide strand. Tropocollagen is the basic building
block of collagen.
• Collagen fibrils are formed by covalent bonds between multiple tropocollagen strands. Collagen fibrils are linked together to form collagen fibers
within the extracellular matrix.
• Most collagen found in the body is Type I, type II or type III and is
produced primarily by fibroblasts, as well as epithelial cells, odontoblasts,
osteocytes, and chondrocytes.
– Note that type I collagen does NOT contain any sulfur amino acids
(e.g. cysteine, homocysteine, and methionine).
Vitamin C, ferrous ions, and alpha-ketoglutarate are important
cofactors involved the hydroxylation of proline residues during collagen synthesis.
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1.2. PROTEINS
Defects in collagen synthesis lead to multiple systemic diseases:
Scurvy is caused by Vitamin C deficiency, resulting in defective collagen synthesis and weakened connective tissue. Signs and symptoms include deterioration and bleeding of the gums, skin discoloration, and poor
wound healing.
Systemic lupus erythematosus and rheumatoid arthritis are autoimmune disorders that develop when the body attacks healthy collagen
fibers.
Osteogenesis imperfecta results from an autosomal dominant genetic defect in the production of type I collagen, causing weak bones and connective tissue. Common signs include multiple fractures, poor wound
healing, hearing loss, and a blue sclera. The condition ranges from mild
symptoms to severe symptoms resulting in death.
Ehler’s Danlos syndrome results from a mutation causing abnormal synthesis, structure, and secretion of primarily type I and type III collagen.
Signs include loose and hyperextended joints, hyperelastic skin, and aortic dissection.
Osteoporosis is caused by reduced levels of collagen in the skin and bones
with aging.
The concentration of hydroxyproline may be used as an estimate
of the amount of collagen present within a given tissue.
Elastin: Synthesis of elastin is very similar to the synthesis of collagen as they
both contain proline and glycine residues (although glycine is more irregularly
spaced in elastin). Elastin fibers are much more elastic than collagen because
they do not contain hydroxylysine or hydroxyproline. The elasticity of the
fibers allows tissues to resume their original shape after significant stretching.
Hemoglobin (Hb): Hemoglobin is a component of red blood cells (RBCs)
and is responsible for transporting O2 to tissues throughout the body.
• Each Hb molecule consists of 4 polypeptide chains (2 alpha and 2 beta
chains) that each have an F e2 containing heme group that irreversibly
binds with oxygen, allowing each Hb molecule to transport four molecules
of O2 (one per heme group). There are over 280 hemoglobin molecules
within one RBC.
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• Iron must be in a ferrous or reduced state (F e2 +) in order for binding to
occur.
• Hb also helps the body eliminate CO2 as waste by picking up CO2 in the
muscles and carrying it to the lungs for exhalation. Approximately 15%
of CO2 is eliminated by Hb (the remainder is eliminated by bicarbonate
within the bloodstream).
Carbon monoxide binds to heme with greater affinity than O2 ,
leading to asphyxiation in carbon monoxide poisoning.
Enamel Proteins: Mature enamel is 95% inorganic hydroxyapatite crystals
composed primarily of calcium and phosphate, 4% water, and 1-2% organic
matrix comprised of proteins essential for enamel formation (may be up to
30% during active tooth development).
• Amelogenins comprise 90% of enamel proteins and are involved in the
organization of enamel rods during tooth development, as well as the
development of cementum. Amelogenin expression ceases when enamel
reaches its full thickness.
Amelogenesis imperfecta is caused by a loss of amelogenin function
during development, resulting in a thin hypoplastic enamel layer
that lacks enamel rods.
• Ameloblastin comprises 5-10% of enamel proteins and is mainly found
during the secretory stage of amelogenesis. Ameloblastin aids in the
elongation of enamel crystals and directs mineralization.
Loss of ameloblastin function results in the detachment of
ameloblasts from dentin and lack of enamel formation.
• Enamelin is the largest and least abundant of the enamel proteins. It is
only present at the growing enamel surface.
• Tuftelin is thought to start the enamel mineralization process.
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1.2. PROTEINS
Enamel is semipermeable and absorbs fluoride ions to form fluorapatite,
causing the tooth to become more acid resistant due to its lower solubility. Remember that enamel is harder than bone and contains hydroxyapaptite crystals that are 4X larger and more firmly packed than bone. The crystals form
keyhole-shaped rods called enamel prisms.
Mechanisms of Enzyme Action
We now introduce concepts related to protein and substrate binding.
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