MOLECULAR BIOLOGY AND DIAGNOSTICS

CHAPTER/LESSON 3: PROTEIN AND MUTATIONS

AMINO ACIDS
 An organic compound that contains both an amino (-NH2) group and a carboxyl group (-COOH) gorup.
 Found in proteins are always alpha-amino acids
 Alpha-amino acids- is an amino acid in which the amino group and the carboxyl group are
attached to the alpha-carbon atom.
 Building blocks of proteins
 Functions:
 Growth, repair, maintenace of all cells are dependent on amino
STRUCTURES AND PROPERTIES
POLAR NON-POLAR
-Hydrophilic (‘’Water-loving’’) -hydrophobic (“Water-fearing”)
-3 Types: -contains one amino agroup, one carboxyl group and
 POLAR NEUTRAL a non polar side chain
 POLAR ACIDIC -consists of Glycine, alanine, valine, leucine,
 POLAR BASIC Isoleucine, proline, phenylalanine, tryptophan and
methionine
POLAR AMINO ACIDS
1. POLAR NEUTRAL AMINO ACIDS
 Another group of amino acids has polar side chains that are electrically neutral (uncharged) at neutral
Ph.
 This group includes SERINE,THREONIN, TYROSINE, CYSTEINE, GLUTAMINE AND
ASPARAGINE.
 SERINE AND THREONINE- polar group is a hydroxyl (-OH) bonded to aliphatic
hydrocarbon groups.
-require such a high Ph
 TYROSINE- hydroxyl group in tyrosine is bonded to an aromatic hydrocarbon group, which
eventually has a protein at a higher Ph.
-hydroxIl group in tyrosine is a phenol, which is a STRONGER ACID.
 CYSTEINE- polar side chain consist of a thiol group(-SH), which can react with other cysteine
thiol groups to form disulfide (-S-S-) bridges in rpotein in an oxidation reaction.
 ASPARAGINE AND GLUTAMINE- have amino groups, which are derived from carboxyl
groups, in their side chains.
-can be considered derivatives of the Group 3 amino acids, glutamic acid and aspartic acid,
respectively.
2. POLAR BASIC AMINO ACIDS
 Another group of amino acis that has positively charged at or near neutral pH
 This includes three positively charged amino acids such as HISTIDINE, LYSINE, AND ARGININE.
 LYSINE- the side chain amino group is attached to an aliphatic hydrocarbon tail.
 HISTIDINE- free histidine, the pka of the side chain imidazole group is 6.0 which is not far
from physiological pH
-found in protonated/unprotonated forms in proteins, and the properties of many proteins depend
on wheter individual histidine residues are or not charged.
  ARGININE- the side chain baisc group, the guanidino group, is more complex in structure than
the amino group, but it is also bonded to an aliphatuc hydrocarbon tail.

NON-POLAR AMINO ACIDS

 PROLINE Has an aliphatic cyclic structuren and the nitrogen is

bonded to two carbon atoms

a.k.a IMINO ACID

 PHENYLALANINE the hydrocarbon group is aromatic rather than

aliphatic

 TRYPTOPHAN the side chain contains an indole ring, which is also

aromatic

 METHIONINE The side chain contains as sulfur atom in addition to

aliphatic hydrocarbon groupings

UNCOMMON AMINO ACIDS

 These are derived from the common amino acids and are produced by modification of the parent
amino acid after the protein is synthesized by the organism in a process called postranslational
modification
 These inclues HYDROXYLYSINE, THYROXINE and HYDROXYPROLINE

HYDROXYPROLINE AND THYROXINE

HYDROXYLYSINE

Differ from the parent amino acids in that
they hydroxyl groups on their side chains.
Found only in a few connective tissue
proteins, such as collagen.
Differs from tyrosine in that it has an extra
Iodine-containing aromatic group on the side
chain.
Produced only in the thyroid gland, formed
by posttranslational modification of tyrosine
residues in the protein thyroglobulin

released as a hormone by proteolysis of

thyroglobulins
 AMINO ACIDS ACCORDING TO ITS ESSENTIALITY
ESSENTIAL AND NONESSENTIAL AMINO ACIDS IN HUMANS
ESSENTIAL NONESSENT
IAL
Arginine° Plays an important role in cell Alanine
division, the healing of wounds,
stimulation of preotein synthesis,
immune function, and the release of
hormones
Histidine Direct precursor of histamine, one of Asparagine
the proteins invloved in the immune
response
Important source of carbon atoms in
the synthesis of purines, one of the
two groups of nitrogen bases that
make up DNA and RNA
Helps manufacture red and white
blood cells and helps to protect the
body from heavy metal toxicity
Isoleucine Helps maintain, heal, and repair Aspartate
muscle tissue, skin, and bones.
Needed for hemoglobin formation
Helps regulate blood glucose levels
and maintain energy levels
Leucine Second most common amino acid Cysteine
found in protein beside glycine
Boosts the healing of muscle, skin,
and bones with the help of valine
and is isoleucine
Simplest of the amino acids and its
involves in the energy-producing
breakdown of glucose.
Plays a major role in the transfer of
nitrogen from peripheral tissue to the
liver.
Helps in reducing the buildup of
toxic substances that are released
into muscle cells when muscle
protein is broken down quickly to
meet energy needs.
Strenghtens the immune system
through production of antibodies
one of the principal and frequently
and the most abundant of the amino
acids involved in the transport of
nitrogen.
Major fnx: convert one amino acid
into another via amination and
transamination.
Required by the nervous sytem and
plays an imporatnat role in the
sythesis of ammonia.
plays a vital role in metabolism
during construction of other amino
acids and metabolites in the citric
acid cycle.
may be essential for infants, elderly,
and individuals with certain
metabolic diseases or malabsorption
syndromes.
Potentially toxic and is catabolized in
 Aids in recovery from surgery and
lowers blood glucose levels
Necessary for the optimal growth of
infants and for nitrogen balance in
adults
Methionine Important amino acid that helps to Glutamate
initiate translation of messenger
RNA by being the first amino acid
incorporated into the N-terminal
position of all proteins
Phenylalanin Promotes alertness and vitality, Glutamine
e elevates mood, decreases paim, aids
memory and learning, and is used to
threat arthritis and depression.
Used by the barin to rpoduce
norepinephrine, a neurotransmitter
that transmits signals between nerve
cells.
Uses an active transport channel to
cross the blood–brain barrier and in
large quantities, interferes with the
production of serotonin, another
neutrotransmitter.
Threonine An importan component in the Glycine
formation of protein, collagen,
elastin (a connective tissue protein ),
and tooth enamel.
Also important in the production of
neurotransmitters and health of the
nervous system.
Tryptophan A precursor for serotonin and Proline
melatonin; a neurohormone and
powerful antioxidant.
the gastrointestinal tract and blood.
Cysteine is absorbed during digestion
as cystine, which is more stable in
the gastrointestinal tract.
linked to epileptic seizures.
A neurotransmitter, is important in
the metabolism of sugars and fats,
and aids transporting potassium into
the spinal fluid.
Most important amino acid in the
body, being involved in more
mtaboliv processes than any other
amino acid.
61% of skeletal muscle tissue is
glutamine.
Converted to glucose when more
glucose is required for energy and
aids in immune function.
Assist in maintaining the proper
acid/alkaline balance in the body,
provides fuel for a healthy digestive
tract, and is the basis of the building
blocks for the synthesisof RNA and
DNA.
simplest amino acid synthesized in
the body and is the only amino acid
that is not optically active because it
has no stereoisomers.
Essential for the synthesis of nucleic
acids, bile acids,proteins, peptides,
purines. ATP, porphyrins,
hemoglobin, glutathione, creatine,
bile salts, glucose, glycogen, and
other amino acids.
Precursor of hydroxyproline, which
is manufactured into collagen,
tendons, ligaments, and heart muscle
by the body.
 Involved in wound healing, plays
important roles in molecular
recognition, and is an important
component in certain medical wound
dressings that use colllagen to
stimulate wound healing.

Valine A constituent of fibrous proteins in Serine
the body.
Needed for muscle metabolism and
coordination, tissue repair, and
maintenance of nitrogen balance.
Needed for the proper metabolism of
fats and fatty acids and plays an
important role in the body’s synthetic
pathways for pyrimidines, purines
(making it important for DNA and
RNA fxn), creatine, and porphyrins.

Used by muscle tissue as an energy

source.

Lysine Tyrosine Metabolically synthesized from the

important amino acid phenylalanine
to become the para-hydroxy
derivative of phenylalanine.

A precursor of adrenal hormones,

epinephrine, norepinephrine, and
dopamine and the thyroid hormones,
including thyroxine.

Important in overall metabolism,

aiding in the of the adrenal,
thyroid, and pituitary glands.

°Although mammals synthesize arginine, they cleave most of it urea.

PEPTIDE BOND AND SMALL PEPTIDES

PEPTIDE BOND SMALL PEPTIDES

An amine bond between amino acids in a protein Biochemically active

Is a covalent bond between the carboxyl group of one Fxns: Hormonal action: OXYTOCIN &
amino acid and the amino group of another amino VASOPRESSIN
acid.
Neurotransmission: ENKEPHALUS
Antioxidant activity: GLUTATHIONE
 PROTEIN STRUCTURE

Primary one-dimensional first step in specifying the three-

dimensional structure of a protein.

Comprised of a linear chain of amino acids.

Secondary Arrangement in space of the atoms in the peptide

backbone.

Have repetitive interactions resulting from

hydrogen bonding between the amide N-H and
the carbonyl groups of the peptide backbone.

Tertiary Arrangement in space of all the atoms in a

protein.

Quaternar The interaction of several polypeptide chains in a

y multi-subunit protein

CLASSIFICATION OF PROTEIN

BASED ON SHAPE

1. FIBROUS- a protein whose molecules have an elongated shape with one dimension with one
dimension much longer than the others.
FIBROUS PROTEIN:

INSULIN Regulatory hormone for controlling glucose mtabolism.

MYOGLOBIN Involved in oxygen storage in muscles.

HEMOGLOBIN Involved in oxygen transport in blood.

TRANSFERRIN Involved in iron transport in blood.

IMMUNOGLOBU Involved in immune system responses.

LIN

2. GLOBULAR- a protein whose molecules have peptide chains that are folded into spherical or
globular shapes.
GLOBULAR PROTEIN:
 KERATIN Found in wool, feathers, hooves, silk, and fingernails.

COLLAGEN Found in blood vessels and ligaments.

ELASTIN BASED
Found in blood vessels andON FUNCTIONS
ligaments.

MYOSIN Found in muscle tissue

1. Their ability to bind small molecules specifically and strongly to themselves.
2. Their ability to bind other proteins, often other like proteins, to form fiber-like structures.
3. Their abilityFound
FIBRIN to bindinto, and often
blood cells become integrated into, cel memrane.
CATALYTIC
3. Enzymes
MEMBRANE- protein
PROTEIN thatparticipate in almostwith
is found associated all the metabolic reacions
a membrane system ofthat occur in cells.
a cell.

DEFENSE Immunoglobulins or antibodies are central to the functioning of the body’s immune
PROTEINS system. They bind to foreign substances, such as bacteria and viruses, to help
combat invasion of the body by foreign particles.
TRANSPORT HEMOGLOBIN-carries oxygen from the lungs to other organs and tissues.
PROTEIN TRANSFERRIN- carries iron from the liver to the bone marrow.
HIGH AND LOW DENSITY LIPOPROTEINS- carriers of CHOLESTEROL in
the bloodstream.
MESSENGER Proteins that transmit signals to coordinate biochemical processes between different
PROTEIN cells, tissues, and organs.
(e.g. insulin, growth hormone and glucagon)
CONTACTILE -Proteins are necessary for all forms of movement.
PROTEIN -Muscles are composed of filament-like contractile proteins that, in response to
nerves stimuli, undego conformation changes that involve contraction and extension.
-Actin and myosin are examples of such proteins
-Human reproduction depends on the movement of sperm. Sperm can “swim”
because of long flagella made up of contractile proteins.
STRUCTURA -proteins confer stiffness and rigidity to otherwise fluid-like biochemical systems.
L -collagen is a component of cartilage.
PROTEIN -a keratin gives mechanical strenghth as well as protective covering to hair,
fingernails, feathers, hooves, and some animal shells.
TRANS- Help control the movement of small molecules and ions thru the cell membrane.
MEMBRANE
PROTEIN
-proteins bind (and store) small moleculesfor future use.
STORAGE -FERRITIN- an iron storage protein, which saves the iron for use in the
PROTEIN biosynthesis of new hemoglobin molecules.
-MYOGLOBIN- an oxygen-storage protein present in msucle: the oxygen so stored
is a reserve oxygen source for working msucle.
REGULATOR -act as sites at which messenger molecules, including messenger proteins such as
Y insulin, can bind and thereby initiate the effect that the messenger “carries”.
PROTEIN
-often the molecules that bind to enzymes (catalytic proteins), thereby turning them
“on” and “off”, and thus controlling enxymatic action.

NUTRIENT -proteins are particularly important in the eraly stages of life, from embryo to infant.
PROTEIN -CASEIN- found in milk
-OVALBUMIN- found in egg white
GLYCOPROTEINS
 A protein that contains carbohydrates or carbohydrate derivatives in addition to amino acids.
 Includes several very important substances; two of these,COLLAGEN and
IMMUNOGLOBULINS.
Types: Collagen
Immunoglobulin
Collagen Immunoglobulin
Presence of carbohydrate units attached by Glycoprotein produced by an organism as a
glycosidic linkages to collagen at its 5- protective responnse to the invasion of
hydroxylysine residues causes collagen to be microorganisms or foreign molecules.
classified as a glycoprotein.
TYPES: G A M B E
Example: breast milk secretion colostrum
(IgA)
````
LIPOPROTEINS
 Conjugated protein that contains lipids in addition to amino acids.
 Major function of such proteins is to help suspend lipids and transport them through the bloodstream.
 Plasma Protein – lipoprotein that is involved in the transport system for lipids in the bloodstream.
Four major classes of Plasma Proteins;
1. Chylomicrons – their function is to transport dietary triacylglycerols from the intestine to the
liver and to adipose tissue.
2. Very-Low-Density Lipoprotein (VLDL) – their function is to transport triacylglycerols
synthesized in the liver to adipose tissue.
3. Low-Density Lipoprotein (LDL) – their function is to transport cholesterol synthesized in the
liver to cells throughout the body.
4. High-Density Lipoprotein (HDL) – their function is to collect excess cholesterol from the body
tissues and transport it back to liver for degradation to bile acids.
Protein Denaturation
 Partial or complete disorganization of protein’s characteristic three-dimensional shape as a result of
disruption of its secondary, tertiary and quaternary structural interactions.

Denaturing Agent Mode of Action

Heat Disrupts hydrogen bonds by making
molecules vibrate too violently; produces
coagulation as in the frying an egg.
Microwave Radiation Causes violent vibration of molecules that
disrupt hydrogen bonds.
Ultraviolet Radiation Operates very similarly to the action of heat
(eg., sunburning)
Violent Whipping or Shaking Causes molecules in globular shapes to
extend to longer lengths, which then entangle
 (eg., beating egg white into meringue)
Detergent Affects R-group interaction
Organic Solvents (eg., ethanol, 2-propanol, Interfere R-group interactions because these
acetone) solvents also can form hydrogen bonds;
quickly denature proteins in bacteria, killing
them (eg., the disinfectant action of 70%
ethanol)
Strong Acid and Bases Disrupt hydrogen bonds and salt bridges;
prolonged action leads to actual hydrolysis of
peptide bonds
Salts of Heavy Metals (eg., salts of Hg2+, Metal ions combine with –SH groups and
Ag+, Pb2+) form poisonous salts
Reducing Agents Reduce disulfide linkages to produce –SH
groups

GENE and GENETIC CODE

Genetic Code
 The determination of the code was done by Marshall Nirenberg and Har Gobind Khorana.
 The relationship between three-nucleotide sequences (codon) in mRNA and amino acid identities.
 It is an assignment of the 64 mRNA codons to specific amino acids
 Codons- three-nucleotide sequence in an mRNA molecule that codes for a specific amino acid.
There are 64 possible codons;
 61 were related to specific amino acids
 3 are stop codons
Feature of Genetic Code
1. It is highly degenerate
 Amino acids are designed by more than one codon.
 Two or more codons exist for all amino acids except Met and Trp.
 SYNONYMS: codons that specify some amino acid
2. There is a pattern to the arrangement of synonyms
 All synonyms for an amino acid fall within a single box.
3. Genetic code is universal
 Same codon specifies same amino acid whether it is a bacterial, a corn plant or human cell.
4. Initiation codon exists
 The existence of “stop” codons suggest the existence of “start” codon.
 AUG: initiator of protein synthesis.
PROTEIN SYNTHESIS: TRANSLATION
Activation of tRNA
 Two steps involved in tRNA activation;
1. An amino acid interacts with an activator molecule to
form a highly energetic complex.
2. Energetic complex reacts with the appropriate
tRNA molecule. A tRNA molecule that has an
amino acid covalently bonded to it at its 3’ end
through an ester linkage.

INITIATION

ELONGATION
TERMINATION

MUTATIONS
 Changes in nucleotide sequences of DNA
 May occur in somatic cells or in gametes
 Chemical and UV radiation can cause mutation
 Can be repaired by enzymes

Classes of Mutations
 1. Spontaneous Mutation
 Happens during DNA replication or incorporation of incorrect nucleotide in a replicating DNA.
 Occurs naturally during DNA replication where changes in DNA sequences happen.

2. Induced
Mutation
 Caused by mutagens which are an environmental factor that changes the DNA sequence.
 Examples; UV lights, X-rays, Gamma rays etc.

Types of Mutations
1. Chromosome Mutation
 Involves changing the structure of a chromosome.
 Involves deletion and addition of the part of a chromosome.
 Five Types
 Deletion – due to breakage, a piece of chromosome is lost.
 Inversion – a segment of a chromosome breaks and flips and reattached again to the
segment.
 Translocation – process where part of the chromosome transfer to another chromosome.
 Nondisjunction – happens when chromosome fails to separate during meiosis. Causes
the gametes to have many or few chromosomes.
 Duplication – happens when the gene sequence is repeated.
2. Gene Mutation
 Change in nucleotide sequence of a gene involving single nucleotide due to copying, errors,
chemicals, viruses etc.
 Types
 Point Mutation – involves 3 types of mutation in a single nucleotide in a gene insertion,
deletion and substitution.
 Substitution – one base pair is replaced by different base pair.
 Insertion – changes the DNA sequence by adding one or more nucleotides to the gene.
 Deletion – changes the DNA sequence by removing at least one nucleotide in a gene,
 Frameshift – this is due to inserting or deleting one or more nucleotides. It drastically
alters the protein and built incorrectly

3. Morphological Mutation
 Generated a visible morphological alterations.
 Examples; size, shape and color
4. Lethal Mutation
 Fatal in nature
 Causes death of an individual
5. Conditional Mutation
 Normal under one condition (permissive) but abnormal under another (restrictive)
 Useful in studying processes such as development and DNA replication.
6. Biochemical Mutation
 Mutation is due to loss or of some biochemical means or nutritional function in cell.