Biochemistry for Medical Technology

UNIT 1: BIOCHEMISTRY IN THE CELL o Lipids (monomeric units: fatty acids, monomeric,
• What is Biochemistry? polyunsaturated, etc.)
o It is a multidisciplinary science that explores the chemistry
of living organisms and the molecular basis for the • The instructions for growth, development, and reproduction
changes occurring in living cells. are encoded in each organism’s nucleic acid.
o Basic principles of biochemistry are common to all living
organisms. CELL: FUNCTIONAL & STRUCTURAL UNIT OF LIFE
o The knowledge of biochemistry can be applied to solve PROKARYOTE EUKARYOTE
problems in medicine, agriculture, environmental “before the nucleus” “true nucleus”
sciences, etc. Contain a well-defined
• It is the study of life (“bio” means life) at the molecular level Single-celled organisms nucleus surrounded by a
o 4 important biomolecules: nuclear membrane
§ Carbohydrates § Nucleic acids Can be single celled, such as
§ Proteins § Lipids Include bacteria and yeasts, and paramecium, or
• 2 important components: cyanobacteria multicellular, such as animals
o Biology and Chemistry (mastery of these two disciplines and plants
are important in the study of biochemistry)
o Additional backgrounds:
§ Molecular Biology, Physiology & Anatomy, and other
sciences like Inorganic and Organic Chemistry, and
Physical Chemistry, and the like
• All living organisms participate in certain processes because
living organisms are able to extract energy from the food
(giving us the nutrients where we can get energy)
o These are all needed for differentiation and reproduction
§ Carbohydrates support the energy requirements of the
cell
§ Proteins to support growth (important attribute of an
organism)
§ Enzymes to function
• Respond to stimuli (changes in their environment)

BIOCHEMICAL FEATURES OF LIVING ORGANISMS

• Cells are the basic structural and functional units of all living
organisms. It is highly organized/ compartmentalized; a
constant energy source is required to maintain a cell’s
ORGANELLE DESCRIPTION
ordered state/ homeostasis.
o Cells make up tissue, tissue makes up organs of, and then • Present in both but more prominent in
the organs make up the different systems of the body. Prokaryotic cells
• Living processes consist of thousands of chemical reactions; • Together with pili and flagellum are made
precise regulation and integration of these reactions are up of polysaccharides (saccharides:
required to maintain life. monomeric unit of carbohydrates)
o Certain biochemical reaction pathways, i.e. glycolysis • Polysaccharide chains cross linked by
and Citric Acid cycle (Krebs cycle), Glycogen proteins coated with lipopolysaccharides
metabolism, gluconeogenesis, ketogenesis, beta Cell Wall • Whereas the pili and flagellum are
oxidation, and a lot more are found in almost all extensions of the cell wall (tiny
organisms. appendages pseudo fit usually for
• All organisms use the same type of (bio)molecules: anchorage, locomotion)
o Proteins (building blocks are amino acids) • Cell wall protects against mechanical and
o Carbohydrates (monomeric units: monosaccharides, hypertonic stress
disaccharides, oligosaccharides, polysaccharides) • Flagellum assists in the movement
o Nucleic acids (DNA & RNA: Nucleotides [1 nucleotide • Pili assists in sexual conjugation
forms polynucleotides]) (DNA & RNA are involved in the Cell • Consists of 40% lipid and 60% protein and
flow of genetic information and gene expression in the Membrane some carbohydrates
central dogma of molecular biomolecules)

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 Biochemistry for Medical Technology
• Semi-permeable boundary that allow for molecules, and ions (i.e. water) filled
entry and exit of nutrients, waste products, the cytoplasm.
and ions o A bacterial chromosome is a single
• Play an important role in DNA replication, circular molecule of naked DNA.
energy production, beta oxidation, etc. • Hair-like projections (flagella and/or pili)
• Contains the chromatin material which is a are also present/attached.
complex of chromosomal DNA and • Structurally more complex
histones (protein part) • Presence of nucleus
Nucleoid
• It consists the genome of an organism o Possess a number of separate
• The storage of genetic information and the chromosomes
site of DNA replication • Filled with diverse structures
• Complexes of 65% RNA and 35% protein o Membrane-bound organelles
Ribosome
• Site of protein synthesis o Cytoplasmic membranes
• Serves as the storage depot of nutrients (as Eukaryotic o Other structures that lack surrounding
small molecules or polymer) Cell membranes
Vacuole
• It is the storage of fueled molecules for • Cell membrane
energy metabolism • Cytoplasm (provides the shape of the cell
• Contains the small molecules (soluble and the region where many metabolic
proteins, enzymes, nutrients, and organic reactions like glycolysis occurs)
Cytoplasm salts dissolved in aqueous solution) o Organelles
• Region where many metabolic reactions o Cytoskeletal elements
occur as in the case of glycolysis o Cytosol
• A flat single membrane • It is a thin film of lipid and protein
Endoplasmic • vesicle of lipid and protein (ribosome [RNA molecules held together by noncovalent
Reticulum & proteins], golgi apparatus [flattened interactions.
vesicle of lipid protein & polysaccharide]) • Functions:
o Define and compartmentalize the cell
Cell o Serve as scaffold for biochemical
Membrane activities
o Provide selectively permeable barrier
(influx and efflux of ions)
o Provide means of transporting solutes
• Play a role in cell-to-cell communication
and detection of external signals
• It is the principal feature that distinguishes
eukaryotic from prokaryotic cells.
• It serves both as repository of genetic
Nucleus information and as the cell’s control
center for reproduction.
ORGANELLE STRUCTURE AND FUNCTION • Processes involved: DNA replication,
• Prokaryotes are considered as ancestor transcription and RNA processing
of eukaryotic cell.
• It plays a critical role in the generation of
• They are unicellular.
useful energy (ATP) derived from the
• There are two major divisions of
breakdown of lipids and carbohydrates.
prokaryotes:
• It contains their own DNA encoding for
o Archaebacteria (ancient class) and Mitochondrion
tRNA, rRNA and some mitochondrial
Eubacteria (true bacteria). proteins.
Prokaryotic • Escherichia coli is the most studied • Most mitochondrial proteins are
Cell prokaryote (especially in mol bio)
synthesized on free ribosomes.
• There are 2 definite membranes in a
• Can harness solar energy to convert CO2
bacterial cell: the cell wall and the
& H2O into carbohydrates;
plasma membrane.
photosynthetic generation of ATP.
• Interior of the cell consists of cytoplasm Chloroplast
• They synthesize their own amino acids,
(watery portion) and nucleoid region.
fatty acids and lipid components of their
o Ribosomes, various RNAs, proteins
own membranes.
(including enzymes) and small

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 Biochemistry for Medical Technology
• Reduction of NO2 — to NH3 also occurs in • It is a small, membrane-enclosed
chloroplast organelles that contain enzymes in
• It is a network of membrane-enclosed variety of metabolic reactions.
tubules and sacs that extends from the • Production and decomposition of H2O2
nuclear membrane throughout the • Oxidative reactions of uric acid
cytoplasm. (overproduction causes gout & arthritis),
• It is the largest organelle in the cell. amino acids and fatty acids.
• Two types: o Women 6 mL/dL
o Rough ER o Men 6.8-7 mL/dL
§ Consists of flattened sheets that is • Synthesis of cholesterol, dolichol and bile
continuous to the outer nuclear acids in specialized cells
membrane. • In plants, glyoxylate cycle and
Endoplasmic
§ Characterized by the presence of photorespiration occurs.
Reticulum
ribosomes on the cytosolic side of • It is a complex networks of protein
the membrane. filaments extending throughout the
o Smooth ER cytoplasm
§ It is tubular in shape. • It determines cell’s shape and internal
§ It is involve in lipid metabolism. organization; responsible for the
Cytoskeleton
§ It is involve in several cellular movement of the cell.
processes: drug detoxification, • Three principal types of cytoskeleton:
carbohydrate metabolism and o Microfilaments
synthesis of neutral fats, o Intermediate filaments
phospholipids and steroids. o Microtubules
• It consists of a series of flattened, • It is also called the microtubule organizing
membranous sacs (cisternae) involved in Centrosome center.
modifying, sorting and packaging of • Its function is to aid cellular division.
Golgi macromolecules for secretion or for • It functions as storage depots for nutrients,
Complex export to other organelles. Vacuole wastes, and specialized materials such as
• Involved in protein processing pigments.
• It is form by fusion of vesicles that bud off
the ER.
• Commonly present in animals
• Single-membrane vessels containing
enzymes for hydrolysis (hydrolase)
• Involved in metabolism of materials
ingested through endocytosis
• It is a membrane-enclosed organelle that
Lysosome
functions to degrade (lyse) materials
taken into the cell and to digest worn out
or unnecessary cell components.
• It contains about 50 different hydrolytic
enzymes that can breakdown
macromolecules.
• Present in animal cell
• In plants it is called glyoxysome
• These are single membrane vesicles
containing catalase (which breaks down
hydrogen peroxide and other oxidative
Peroxisome
enzymes such as glutathione peroxidase
and glutathione reductase) • With this, we would understand that the DNA, RNA, proteins,
• Involved in oxidation reactions of and some carbohydrates serve as informational molecules
metabolism of nutrients using oxygen to and that they carry instructions for the direction and control
generate hydrogen peroxide of biological processes.
• The genetic information in DNA flows through the sequence:
DNA to RNA à RNA to Proteins à Proteins to Cellular Processes

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 Biochemistry for Medical Technology
Watch: https://dnalc.cshl.edu/resources/3d/cellsignals.html
CELL SIGNALS

Book: Bettelheim 2020 edition

END OF UNIT 1

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 Biochemistry for Medical Technology
UNIT 2: PROTEINS
• Proteins serve many functions, including the following:
FUNCTION DESCIRPTION
Collagen and keratin are the chief
1. Structure
constituents of skin, bone, hair, and nails.
Virtually all reactions in living systems are
2. Catalysts
catalyzed by proteins called enzymes.
Muscles are made up of proteins called
3. Movement
myosin and actin.
• A comparison of the configuration of L-alanine and D-
Hemoglobin transports oxygen from the
glyceraldehyde (as Fischer projections):
4. Transport lungs to cells, other proteins transport
molecules across cell membranes.
Many hormones are proteins, among them
5. Hormones insulin, oxytocin, and human growth
hormone.
Blood clotting involves the protein
6. Protection fibrinogen; the body used proteins called
antibodies to fight disease.
Casein in milk and ovalbumin in eggs store
7. Storage nutrients for newborn infants and birds.
Ferritin, a protein in the liver, stores iron.
Certain proteins not only control the
8. Regulation expression of genes, but also control when
gene expression takes place. PROTEIN-DERIVED α-AMINO ACIDS
• Nonpolar side chains
• Proteins are divided into two types: o Each ionizable group is shown in the form present in
FIBROUS PROTEINS GLOBULAR PROTEINS highest concentration at pH 7.0
Insoluble in water and are More soluble in water and are
mainly used for structural used mainly for nonstructural
purposes purposes

AMINO ACIDS
• Amino acid: A compound that contains both an amino group
and a carboxyl group.
o α-Amino acid: An amino acid in which the amino group is
on the carbon adjacent to the carboxyl group.
o Although α-amino acids are commonly written in the un-
ionized form, they are more properly written in the
zwitterion (internal salt)form.

• Polar side chains (at pH 7.0)

CHIRALITY OF α-AMINO ACIDS

• With the exception of glycine, all protein-derived amino acids
have at least one stereocenter (the α-carbon) and are chiral.
o The vast majority of α-amino acids have the L-
configuration at the α-carbon. • Acidic and basic side chains (at pH 7.0)

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1. For 19 of the 20, the α-amino group is primary; for proline,

it is secondary.
2. With the exception of glycine, the α-carbon of each is a
stereocenter.
3. Isoleucine (left) and threonine (right) contain a second
stereocenter.

IONIZATION VS. pH
• The net charge on an amino acid depends on the pH of the
solution in which it is dissolved.
o If we dissolve an amino acid in water, it is present in the
aqueous solution as its ZWITTERION.
o If we add a strong acid such as HCl to bring the pH of the
solution to 0.0, the strong acid donates a proton to the -
COO- of the zwitterion turning it into a positive ion.

o If we add a strong base such as NaOH to the solution and

bring its pH to 14, a proton is transferred from the NH3+ CYSTEINE
group to the base turning the zwitterion into a negative • The -SH (sulfhydryl) group of cysteine is easily oxidized to an -
ion. S-S- (disulfide).

o To summarize:

ISOELECTRIC POINT (pI)

• Isoelectric point, pI: The pH at which the majority of molecules
of a compound in solution have no net charge. PHE, TRP, AND TYR
• The amino acids phenylalanine, tryptophan, and tyrosine
have aromatic rings on their side chains.
• Tryptophan is the precursor to the neurotransmitter serotonin.

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PEPTIDES DESCRIPTION
A short polymer of amino acids joined by
TYR AND PHE
1. Peptide peptide bonds; they are classified by the
• Phenylalanine and tyrosine are precursors to norepinephrine
number of amino acids in the chain.
and epinephrine, both of which are stimulatory transmitters.
A molecule containing two amino acids
2. Dipeptide
joined by a peptide bond.
A molecule containing three amino acids
3. Tripeptide
joined by peptide bonds.
A macromolecule containing many
4. Polypeptide
amino acids joined by peptide bonds.
A biological macromolecule containing
5. Protein at least 30 to 50 amino acids joined by
OTHER AMINO ACIDS peptide bonds.
• Hydroxylation (oxidation) of proline, lysine, and tyrosine,
respectively and iodination for tyrosine, give these • The individual amino acid units are often referred to as
uncommon amino acids. “residues”.

PEPTIDE BOND
• A peptide bond is typically written as a carbonyl group
bonded to an N-H group. Linus Pauling, however, discovered
that there is about 40% double bond character to the C-N
bond and that a peptide bond between two amino acids is
planar, which Pauling explained using the concept of
resonance.

WRITING PEPTIDES
• By convention, peptides are written from the left to right,
beginning with the free -NH3+ group and ending with the free
-COO- group.
• C-terminal amino acid: The amino acid at the end of the
chain having the free -COO- group.
• N-terminal amino acid: The amino acid at the end of the
PEPTIDES
chain having the free -NH3+ group.
• In 1902, Emil Fischer proposed that proteins are long chains of
• Alternatively they are referred to as the C-terminus and
amino acids joined by amide bonds.
the N-terminus.
o Peptide bond (peptide linkage): The special name given
to the amide bond between the α-carboxyl group of one
PEPTIDES
amino acid and the α-amino group of another.
• A small peptide showing the direction of the peptide chain
(N-terminal to C-terminal)

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 Biochemistry for Medical Technology
• The hormone insulin consists of two polypeptide chains, A and
B, held together by two disulfide bonds. The sequence shown
here is for bovine insulin.

PEPTIDES AND PROTEINS

• Proteins behave as zwitterions.
• Proteins have an isoelectric point, pI. • How important is the exact amino acid sequence?
o At its isoelectric point, the protein has no net charge. o Human insulin consists of two polypeptide chains having a
o At any pH above (more basic than) its pI, it has a net total of 51amino acids; the two chains are connected by
negative charge. two interchain disulfide bonds.
o At any pH below (more acidic than) its pI, it has a net o Differences between four types of insulin.
positive charge.
o Hemoglobin, for example, has an almost equal number of
acidic and basic side chains; its pI is 6.8.
o Serum albumin has more acidic side chains; its pI is 4.9.
o Proteins are least soluble in water at their isoelectric points
and can be precipitated from solution when pH = pI.

LEVELS OF STRUCTURE

LEVEL OF STRUCTURE DESCRIPTION

• The sequence of amino acids
in a polypeptide chain.
PRIMARY STRUCTURE • Read from the N-terminal
amino acid to the C-terminal • Vasopressin and oxytocin are both nonapeptides but have
quite different biological functions.
amino acid.
• Vasopressin is an antidiuretic hormone.
• Conformations of amino acids
• Oxytocin affects contractions of the uterus in childbirth and
in localized regions of a
the muscles of the breast that aid in the secretion of milk.
polypeptide chain.
SECONDARY STRUCTURE • The structures of vasopressin an oxytocin.
• Examples are α-helix, β-
pleated sheet, and random
coil.
• The complete three-
TERTIARY STRUCTURE dimensional arrangement of
atoms of a polypeptide chain.
• The spatial relationship and
interactions between subunits
QUATERNARY STRUCTURE
in a protein that has more than
one polypeptide chain.

PRIMARY STRUCTURE
• Primary structure: The sequence of amino acids in a
polypeptide chain.
• The number peptides possible from the 20 protein-derived
amino acids is enormous.
o There are 20 x 20 = 400 dipeptides possible.
o There are 20 x 20 x 20 = 8000 tripeptides possible.
o The number of peptides possible for a chain of n amino
acids is 20n.
o For a small protein of 60 amino acids, the number of
proteins possible is 2060 = 1078, which is possibly greater
than the number of atoms in the universe!

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SECONDARY STRUCTURE β-PLEATED SHEET
• Secondary structure: Conformations of amino acids in
localized regions of a polypeptide chain.
o The most common types of secondary structure are α-helix
and β-pleated sheet.
o α-Helix: A type of secondary structure in which a section
of polypeptide chain coils into a spiral, most commonly a
right-handed spiral.
o β-Pleated sheet: A type of secondary structure in which
two polypeptide chains or sections of the same
polypeptide chain align parallel to each other; the chains
may be parallel or antiparallel.

α-HELIX

• In a section of β-pleated sheet;

o The six atoms of each peptide bond of a β-pleated sheet
lie in the same plane.
o The C=O and N-H groups of the peptide bonds from
adjacent chains point toward each other and are in the
same plane so that hydrogen bonding is possible between
them.
o All R- groups on any one chain alternate, first above, then
below the plane of the sheet, etc.

• In a section of α-helix
o There are 3.6 amino acids per turn of the helix.
o The six atoms of each peptide bond lie in the same plane.
o The N-H groups of peptide bonds point in the same
direction, roughly parallel to the axis of the helix.
o The C=O groups of peptide bonds point in the opposite
direction, also roughly parallel to the axis of the helix.
o The C=O group of each peptide bond is hydrogen
bonded to the N-H group of the peptide bond four amino
acid units away from it.
o All R- groups point outward from the helix.
• The model is an α-helix section of polyalanine, a polypeptide
derived entirely from alanine. The intrachain hydrogen bonds
that stabilize the helix are visible as the interacting C=O and
N-H bonds.

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• Many globular proteins contain all three kinds of secondary TERTIARY STRUCTURE
structure in different parts of their molecules: α-helix, β- • Tertiary structure: the overall conformation of an entire
pleated sheet, and random coil polypeptide chain.
• Schematic structure of the enzyme carboxypeptidase. The β- • Tertiary structure is stabilized in four ways:
pleated sheet sections are shown in blue, the α-helix portions o Covalent bonds as for example, the formation of disulfide
in green, and the random coils as orange strings. bonds between cysteine side chains.
o Hydrogen bonding between polar groups of side chains,
as for example between the -OH groups of serine and
threonine.
o Salt bridges, as for example, the attraction of the -NH3+
group of lysine and the -COO- group of aspartic acid.
o Hydrophobic interactions, as for example, between the
nonpolar side chains of phenylalanine and isoleucine.

QUATERNARY STRUCTURE
• The Collagen Triple Helix
• Quaternary structure: The arrangement of polypeptide chains
into a noncovalently bonded aggregation.
o The individual chains are held together by hydrogen
bonds, salt bridges, and hydrophobic interactions.
• Hemoglobin
o Adult hemoglobin: Two alpha chains of 141 amino acids
each, and two beta chains of 146 amino acids each.
o Fetal hemoglobin: Two alpha chains and two gamma
chains. Fetal hemoglobin has a greater affinity for oxygen
than does adult hemoglobin.
o Each chain surrounds an iron-containing heme unit.

• Integral membrane proteins form quaternary structures in

which the outer surface is largely nonpolar (hydrophobic)
and interacts with the lipid bilayer.
• Integral membrane protein of rhodopsin, made of α-helices.

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DENATURATION & REFOLDING AND UNFOLDING
• The process of destroying the native conformation of a
protein by chemical or physical means
• Causes the protein to lose its native secondary, tertiary and
quaternary structures
• The noncovalent interactions that maintain the 3-D structure
of proteins are weak, thus can be disrupted easily
• The unfolding of a protein (i.e., disruption of the protein
structure is called denaturation)

MODES OF PROTEIN DENATURATION

• Some denaturations are reversible, while others permanently
damage the protein
• Denaturation and reduction of disulfide bonds –S-S- are
combined to effect complete disruption of tertiary structure
of proteins
• Denaturants – heat, pH, 6M urea, detergents, acids/bases,
salts, reducing agents, heavy metals, alcohol

HEAT
• Increase in temperatures favors vibrations; increases the
kinetic energy within the energy and become great enough
to disrupt the bonds (tertiary structure) of proteins
• Affected regions: hydrogen bonds
• Ex. Proteins in eggs denature and coagulate during cooking

• An integral membrane protein from the outer mitochondrial pH

membrane forming a β-barrel from eight β-pleated sheets. • High or low extreme pH destabilizes electrostatic interactions
that normally stabilize the native, active form of the protein
that may denature it
• Affects the chemistry of amino acids
• Protonation of the amin acid residues
• Acids/bases affect salt bridges and hydrogen bonds

SALTS OR UREA (NH2-CO-NH2)

• Affects hydrogen bonds, affects a protein that contains
antiparallel beta-sheets leading random coil
• Interferes with the structure of solvent water, attenuating the
hydrophobic effect and causes the protein to unfold.
o When the solvent is removed, the proteins renature
• Urea forms hydrogen bonds with the protein that are stronger
than those within the protein itself
• Salts affect salt bridges

DETERGENTS: SURFACE ACTIVE AGENTS (SDS)

• Affected regions: hydrophobic regions
• Denatures the proteins by disrupting hydrophobic interaction
• If detergent is charged, it can disrupt electrostatic
interactions within the protein
• Ex the hydrophobic portion of a detergent allows the
molecule to partition into the apolar lipid bilayer during the
solubilization of membrane proteins

REDUCING AGENT (2-MERCAPTOETHANOL)

• HS-CH2-CH2-OH

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• Reduces/cleaves disulfide bridges to two sulfhydryl groups of
cysteine resides
• Both the tertiary and quaternary structure of proteins can be
disrupted

HEAVY METALS
• Pb2+, Hg2+, Cd2+, Ag+
• Affected regions: disulfide bonds
• Attacks the –SH groups, forming salt bridges
• Metal ions can also combine with carboxylate ion on R-
groups, preventing their participation in salt bridges
• Use of raw egg white and milk

ALCOHOL
• Coagulates proteins
• Affected regions: physical structure of cell membrane (most
fluid membrane – low in cholesterol)
• Disrupts the intramolecular hydrogen bonding between the
side chains, which is essential to maintain the tertiary protein
structure
• Can also interact with the hydrophobic residues in a protein,
destroying its hydrophobic core and resulting in denaturation

END OF UNIT 2

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