Chapter 5 (Biomolecules)  Glutamic acid

- Is replaced by a valine residue in sickle

PROTEIN STRUCTURE cell hemoglobin.

 Primary Structure
 Isoleucine
- Consists of the sequence of the amino
- Positioned in 3 of oxytocin replaced by
acids that makes up the chain. It
phenylalanine in vasopressin.
always involve more than just the
 Leucine
number and kinds of amino acids
- In position of 8 of oxytocin is replaced
present; it also involves the order of
with arginine.
attachment of the amino acids to
 Anemia
each other through peptide bond.
- It is cause if the body defense destroys
 Human insulin
the clogging cells and the loss of blood
- Consists of two chains having a total
cell.
of 51 amino acids. Chain A is
 Secondary structure
composed of 21 amino acids residues
- Is the repeating pattern of protein that
while chain B is composed of 30 amino
can fold or align themselves.
acid residues.
 Alpha helix /a-helix
 Disulfide bond
- A single chain twist in such manner that
- A bond that connects chain A and chain
its shapes resembles a coiled spring. It
B.
shape is maintained by means of
 Insulin
numerous intramolecular hydrogen
- Is necessary for proper utilization of
bond that exist between the backbone
carbohydrates.
–C=O and amino groups.
 Vasopressin
 Beta-pleated helix/ b-pleated sheet
- Is an antidiuretic hormone. It increases
- The orderly arrangement of protein
the amount of water reabsorbed by the
chain is maintained by intermolecular
kidney and raises blood pressure. It alos
hydrogen bond. It can occur between
stimulate uterine contraction, but much
molecule when polypeptide chains runs
less so than oxytocin.
parallel or antiparallel.
 Oxytocin
 Parallel b-pleated sheet
- Has no effect on water in the kidney an
- All N-terminals end on one side.
slightly lower blood pressure. It affects
 Antiparallel b-pleated sheet
contraction of the uterus during
- Neighboring N-terminal ends on
childbirth and the muscle in the breasts
opposite sides.
that aids in the secretion of milk.
 Hydrogen bonding
 Sickle cell anemia
- It stabilizes secondary structure. Is
- a fatal disease that is cause if there is a
between backbone –C=O and H-N –
change in only one amino acid in a
group. This is distinction between
chain of 146.
secondary and tertiary structure.
-
 Keratin
- A fibrous protein of hair, fingernails,
horns and wools, is one protein that is
predominantly a-helix structure.
 Silk
- Is made up of fibroin, another fibrous
protein that exist mainly in the B-
pleated pattern.
 Collagen
- Is the structural protein of the
connective tissue (bone, cartilage,
tendon, skin and aorta), where it
provides strength and elasticity. It is the
most abundant protein in the body
making up about the 30% by weight of
all the body protein.
 B-pleated pattern
- A pattern in which a fibroin mainly exist.
 Tertiary structure
- Is the complete three-dimensional
arrangement of the atoms in a protein
molecule. It is stabilized by five
chemical forces.
 Covalent bond
- Most often involved in stabilizing
tertiary structure of protein.
 Disulfide bond
- The covalent bond is often used to
stabilized tertiary structure. It is formed
from the –SH side chain of two residues
in one chain or in different chain.
 Hydrogen bonding
- Stabilized tertiary structure of protein
formed between polar groups of the
side chain or between side chain and
peptide backbone.
 Salt bridges
- Also called electrostatic attraction occur
only between two amino acids with
ionized side chain, that is between an
acidic amino acid and basic amino acid,
each in its ionized form. It is a simple
ion-ion attraction that hold the two
together.
 Hydrophobic interaction
- It is a series of interaction in which the
non-polar groups prefers to interact
with each other excluding water from
this region.
 Polar group
- Usually turns outward, towards the
aqueous solvent.
 Non-polar group
- Turns inward away, away from the
water molecule.
 Metal Ion coordination
- Two side chains with the same charges
would normally repel each other, but
they can also be linked via metal ion.
 Quaternary structure
- It is the highest level of organization
which applies to protein with more than
one polypeptide chain. It is spatial
relationship and interaction between
subunits in a protein that has more than
one polypeptide chain. It determines
how the different subunits of the
protein fits into an organized whole.
 Human hemoglobin molecule
- Best example of protein that exists in
quaternary structure. Composed of 574
amino acids residue.
 Heme unit
- A non-amino group that surrounds each
globin chain.
 Conjugated protein
- Proteins that contain non-amino
portion.
 Prosthetic group
- The non-amino acid portion of a
conjugated protein.
 Globin
- Each protein of hemoglobin molecule
 Heme
- A red pigmented molecule
 Tropocollagen
- A triple helix units that constitute the
soluble form of collagen; they are
stabilized by hydrogen bonding
between the backbones of the three
chain. It is found only in fetal and young
connective tissues.
 Integral membrane protein
- Is a protein molecule that traverses
partly or completely a membrane
bilayer.
 Denaturation
- Is the loss of the secondary, tertiary,
and quaternary structures of a protein
by a chemical or physical agent that
leaves the primary structures intact. It
involves the uncoiling of the protein
molecule which causes loss of its
biological function.
 Denaturant
- Any physical or chemical agents that
destroys the stabilizing structures of
protein changing their configuration.
 Physical denaturant
- Includes heat, radiation, an ultraviolet
rays that denature bacteria by killing
them.
 Chemical denaturant
- Include alcohol, detergent, strong
mineral acids, strong alkaloidal reagent,
reducing agent, and salts of heavy
metals.
 Coagulation
- The process in which colloidal particle
come together to form larger mass.
 Precipitation
- The process in which small solid particle
are formed in a liquid or solution.
 Enzymes
- Are biological protein that catalyzes
that catalyzes the chemical reactions
that makes life possible. A compound
usually a protein that acts as catalyst for
a biochemical reaction.
 Urease
- The enzyme that catalyzes only the
hydrolysis of urea but not of other
amide even closely related to urea.
 Trypsin
- An enzyme that catalyze the cleavage or
hydrolysis of peptide bond or protein
molecule but not every peptide bond
only those carboxylic side of lysine and
arginine residue.
 Carboxypeptidase
- The enzyme that specifically catalyze
the hydrolysis of only the last amino
acid residue at the C-terminal of a
protein chain.
 Substrate
- Is the reactant in an enzyme catalyzed
reaction. It is the substance that an
enzyme work or act on during enzyme
catalyzed reaction.
 Oxidoreductase
- Is an enzyme that catalyzes an
oxidation-reduction reaction.
 Reducing agent
- Electron donor
 Oxidizing agent
- Electron acceptor
 Lactate dehydrogenase
- Is an oxidoreductase enzyme that
removes hydrogen atom from a
molecule.
 Transferase
- Is an enzyme that catalyzes the transfer
of a functional group from one
molecule to another.
 Transaminase
- Catalyzes transfer of an amino from one
molecule to another.
 Kinases
- Catalyzes transfer of phosphate group
from ATP to give ADP and a
phosphorylated product during
phosphorylation reaction.
 Alanine transaminase
- A transferase enzyme that catalyze the
transfer of amino group form L-alanine
to a-ketoglutarate to form pyruvate and
L-glutamate.
 Hydrolase
- Is an enzyme that catalyzes hydrolysis
reaction in which the addition of water
molecule to a bond causes the bond to
cleave.
 Hydrolysis
- Is the cleavage or splitting of a single
molecule to two distinct molecules in
the presence of water. It is the central
process of digestion.
 Carbohydrase
- Catalyzes the breakdown of
carbohydrates into simple sugar.
 Proteases
- Catalyzes the breakdown of protein into
amino acids.
 Lipase
- Catalyze the breakdown of lipids into
glycerol and fatty acids.
 Lyases
- Is an enzyme that catalyzes the splitting
of molecule into different molecule
without the use of water. It catalyzes
the non-hydrolytic cleavage. Also
catalyze the addition of a group to a
double bond or removal of groups to
create a double bond. (pyruvate
decarboxylase)
 Carbon-carbon bond cleavage
- The prevalent reaction of lyases.
 Aldolase
- A lyases enzyme that catalyzes the
most common reaction of non-
hydrolytic in which the splitting of
fructoses 1, 6-biphosphate
glycealdehydes-3-phosphate and
dihydroxyacetone phosphate during
glycolytic pathway.
 Isomerase
- Is an enzyme that catalyzes the
isomerization (rearrangement of atoms)
of a substrate in a reaction, converting
it into a molecule isomeric to itself.
 Intramolecular hydrogen shift changing
the location og hydrogen bond
- The most prominent reaction of this
type of aldose-ketose isomerization ; an
important reaction in glycolysis.
 Intramolecular rearrangement of
functional group
- This type of reaction involves the
rotation of group at the chiral carbon
forming D- or L-isomer.
 Trioseisomerase
- The enzyme that catalyzes the
intramolecular hydrogen shift changing
the location of double bond.
 Alanine racemase
- The enzyme that catalyzes the
reactionof L-alanine to D-alanine.
 Mutase
- An enzyme that belongs to a subclass of
isomerase.
 Phospolyceromutase
- Catalyzes the shift of phosphate group  Activators
from C3 of 3-phosphoglycerate to C2 - The substance that acts on inactive
yield and isomer of 2-phosphoglyerate. enzyme making it active.
 Ligase/synthetase  Inhibition
- An enzyme that catalyzes the joining of - Any process that makes an active
two molecules using energy form ATP enzyme less active or inactive.
to form new chemical bond.  Inhibitors
 Glutamine synthetase - Are compound that accomplished the
- Catalyzes the joining of amino group inhibition process.
from ammonium ion to glutamate to
form glutamine at the expense of an
ATP molecule as an energy source.
 Simple enzyme
- Some enzyme that consist of
polypeptide only such as chymotrypsin,
pepsin and trypsin.
 Prosthetic group
- An conjugated protein containing non-
protein portion are called as.
 Apoenzyme
- The protein or polypeptide portion of
the enzyme.
 Co-factor
- If the prosthetic group of enzyme is an
inorganic compound.
 Coenzyme
- An organic co-factors.
 Holoenzyme
- A complete enzyme that is formed by
apoenzyme together with co-factoe and
con-enzyme.
 Active site
- The specific portion of the enzyme to
which the substrate binds during the
reaction.
 Proenzyme or zymogen
- The inactive forms of enzyme.
 Activation
- Any process that makes an inactive
enzyme active.