PRE FI: STRUCTURAL ORGANIZATIONS OF PROTEINS Flashcards
- linear sequence of amino acids
- it determines the identity of protein, molecular
structure, function and binding capacity
PRIMARY STRUCTURE
- Arrangement of atoms of backbone in space.
- local interactions between stretches of a polypeptide
chain and includes α-helix and β-pleated sheet
structures
SECONDARY STRUCTURE
- actual 3-dimentional structure or folding pattern
- responsible for physical and chemical properties of proteins
- Results from the interactions between amino acid side chains (R groups) that are widely separated from each other.
Tertiary Structure
- refers to the organization among the various
polypeptide chains in a multimeric protein - Highest level of protein organization
- Present only in proteins that have 2 or more
polypeptide chains (subunits) - Subunits are generally independent of each other - not covalently bonded
- Proteins with quaternary structure are often referred to as oligomeric proteins
- Contain even number of subunits
Quaternary Structure
Proteins with quaternary structure are often referred to as ______________
OLIGOMERIC PROTEINS
- the partial or complete disorganization of a protein’s characteristic three-dimensional shape as a result of disruption of its secondary, tertiary, and quaternary structural interactions.
- because the biochemical function of a protein depends on its three-dimensional shape, the result of denaturation is loss of biochemical activity
(loss of 3D shape = loss of biochemical activity) - does not affect the primary structure of a protein
PROTEIN DENATURATION
ESSENTIAL AMINO ACIDS
- HISTIDINE
- ISOLEUCINE
- LEUCINE
- METHIONINE
- PHENYLALANINE
- THREONINE
- TRYPTOPHAN
- VALINE
- LYSINE
CONDITIONALLY NON-ESSENTIAL AMINO ACIDS
- ARGININE
- ASPARAGINE
- GLUTAMINE
- GLYCINE
- PROLINE
- SERINE
- TYROSINE
NON - ESSENTIAL AMINO ACIDS
- ALAMINE
- ASPARTATE
- CYSTEINE
- GLUTAMATE
Required for growth in children and is not essential for adults (only considered essential when a person is ill or stressed)
Conditionally Non-Essential Amino Acids
21st Amino Acid:
Selenocysteine/SEC
FUNCTIONAL GROUPS AND THE AMINO ACIDS THEY
CONTAIN:
- Cysteine, Methionine
A. Sulfur/sulfhydryl group
B. Aromatic group
C. Imidazole ring
D. Guanidine group
E. Indole group
Sulfur/sulfhydryl group
FUNCTIONAL GROUPS AND THE AMINO ACIDS THEY
CONTAIN:
- Phenylalanine, Tyrosine, Tryptophan
A. Sulfur/sulfhydryl group
B. Aromatic group
C. Imidazole ring
D. Guanidine group
E. Indole group
Aromatic group
FUNCTIONAL GROUPS AND THE AMINO ACIDS THEY
CONTAIN:
- Histidine
A. Sulfur/sulfhydryl group
B. Aromatic group
C. Imidazole ring
D. Guanidine group
E. Indole group
Imidazole ring
FUNCTIONAL GROUPS AND THE AMINO ACIDS THEY
CONTAIN:
- Arginine
A. Sulfur/sulfhydryl group
B. Aromatic group
C. Imidazole ring
D. Guanidine group
E. Indole group
Guanidine group
FUNCTIONAL GROUPS AND THE AMINO ACIDS THEY
CONTAIN:
- Tryptophan
A. Sulfur/sulfhydryl group
B. Aromatic group
C. Imidazole ring
D. Guanidine group
E. Indole group
Indole group
SOME CLASSIFICATIONS OF PROTEINS ACCORDING TO THEIR BIOLOGICAL FUNCTION:
o E.g., Casein, Ovalbumin, Gluten, Ferritin (Iron)
o Casein and Ovalbumin also function as Nutrient
proteins
A. Storage proteins
B. Structural proteins
C. Messenger proteins
D. Transport proteins
E. Respiratory pigments
Storage proteins
SOME CLASSIFICATIONS OF PROTEINS ACCORDING TO THEIR BIOLOGICAL FUNCTION:
o E.g., Collagen, Keratin, Elastin, Actin, Myosin
A. Storage proteins
B. Structural proteins
C. Messenger proteins
D. Transport proteins
E. Respiratory pigments
Structural proteins
SOME CLASSIFICATIONS OF PROTEINS ACCORDING TO THEIR BIOLOGICAL FUNCTION:
o E.g., Hormones
A. Storage proteins
B. Structural proteins
C. Messenger proteins
D. Transport proteins
E. Respiratory pigments
Messenger proteins
SOME CLASSIFICATIONS OF PROTEINS ACCORDING TO THEIR BIOLOGICAL FUNCTION:
o o E.g., Albumin, Transferrin (transport Iron),
Ceruloplasmin (transport Copper)
A. Storage proteins
B. Structural proteins
C. Messenger proteins
D. Transport proteins
E. Respiratory pigments
Transport proteins
SOME CLASSIFICATIONS OF PROTEINS ACCORDING TO THEIR BIOLOGICAL FUNCTION:
o E.g., Hemoglobin, Myoglobin (also classified as a
storage protein), Hemerythrin, Hemocyanin
A. Storage proteins
B. Structural proteins
C. Messenger proteins
D. Transport proteins
E. Respiratory pigments
Respiratory pigments
- catalyze the biochemical reactions by participating as a catalyst they are simply responsible for INCREASING THE RATE OF REACTION
- catalyze a reaction by binding substrate to the active site and various non-covalent interactions are formed and broken which provides energy
- This energy from bond formation and breakage
counteracts the activation barrier THUS LOWERING THE ACTIVATION ENERGY
ENZYMES
ENZYMES LOWER THE ACTIVATION ENERGY OF
CHEMICAL REACTIONS.
TRUE OR FALSE?
TRUE
the amount of energy that must be put in for the reaction to begin
ACTIVATION ENERGY
ENZYME CLASSIFICATION
* catalyze an OXIDATION – REDUCTION REACTION; oxidation and reduction reactions are always linked to one another (oxidase, dehydrogenase)
* requires a coenzyme that is either oxidized or reduced as the substrate in the reaction
* E.g., Lactate dehydrogenase is an oxidoreductase and NAD+ is the coenzyme in this reaction.
OXIDOREDUCTASES
ENZYME CLASSIFICATION
* catalyze the TRANSFER OF A FUNCTIONAL GROUP from one molecule to another (transferase, kinase)
Two major subtypes:
o Transaminases
o Kinases
o Alanine transaminase is a transaminase enzyme. It is also called ALANINE AMINOTRANSFERASE and was formerly called SERUM GLUTAMATE-PYRUVATE TRANSAMINASE or SERUM GLUTAMIC-PYRUVIC TRANSAMINASE
TRANSFERASES
SUBTYPE OF TRANSFERASE
- catalyze transfer of an AMINO group to a substrate
TRANSAMINASES
SUBTYPE OF TRANSFERASE
- catalyze transfer of a PHOSPHATE group from
adenosine triphosphate (ATP) to a substrate
KINASES
ENZYME CLASSIFICATION
* catalyzes a HYDROLYSIS REACTION (addition of a water molecule to a bond to cause bond breakage) (nuclease, protease)
* Hydrolysis reactions are central to the process of
digestion:
o Carbohydrases hydrolyze glycosidic bonds in
oligo- and polysaccharides
o Proteases effect the breaking of peptide linkages
in proteins (e.g., Pepsin, Trypsin, Chymotrypsin,
Papain)
o Lipases effect the breaking of ester linkages in
triacylglycerols
HYDROLASES
ENZYME CLASSIFICATION
* catalyze the addition of a group to a double bond or the removal of a group to form a double bond in a manner that does not involve hydrolysis or oxidation (decarboxylase, aldolase)
LYASES
LYASES
- effects the REMOVAL of the components of water from a double bond
Dehydratase
LYASES
- effects the ADDITION of the components of water to a double bonds
Hydratase
ENZYME CLASSIFICATION
* catalyze the ISOMERIZATION (REARRANGEMENT OF ATOMS) of a substrate in a reaction, converting it into a molecule isomeric with itself.
ISOMERASES
ENZYME CLASSIFICATION
- catalyze the formation of a bond between two
molecules involving ATP hydrolysis:
o ATP hydrolysis is required because such reactions
are energetically unfavorable
o Require the simultaneous input of energy obtained by a hydrolysis of ATP to ADP
EX: DNA ligase
LIGASE
a measure of the rate at which enzyme converts substrate to products in a biochemical reaction
ENZYME ACTIVITY
FACTORS AFFECTING ENZYME ACTIVITY
- TEMPERATURE
- pH
- SUBSTRATE CONCENTRATION
- ENZYME CONCENTRATION
Higher temperature = higher kinetic energy = increase in number of reactant collisions, therefore there is higher activity
TRUE OR FALSE?
TRUE
temperature at which the rate of enzyme catalyzed reaction is maximum
Optimum temperature
Optimum temperature for human enzymes is
37ºC (body temperature)
Increased temperature (high fever) leads to
decreased enzyme activity
Drastic changes in pH can result in denaturation of
proteins
TRUE OR FALSE?
TRUE
pH at which enzyme has maximum activity
Optimum pH
Most enzymes have optimal activity in the pH range
of
7.0 - 7.5
Most enzymes have optimal activity in the pH range
of 7.0 - 7.5
o Exception:
DIGESTIVE ENZYMES LIKE PEPSIN AND TRYPSIN
Pepsin: Optimum pH =
2.0
Trypsin: Optimum pH =
8.0
at a CONSTANT enzyme concentration, the enzyme activity increases with increased substrate concentration
TRUE OR FALSE
TRUE
the concentration at which it reaches its MAXIMUM RATE and all of the ACTIVE SITES ARE FULL
Substrate saturation
Number of SUBSTRATE MOLECULES converted to PRODUCT PER SECOND PER ENZYME molecule under conditions of optimum temperature and
pH
Turnover Number
Enzymes are consumed in the reactions they
catalyze
TRUE OR FALSE?
FALSE, THEY ARE NOT CONSUMED
at a CONSTANT substrate concentration, enzyme activity increases with increase in enzyme concentration
TRUE OR FALSE?
TRUE
the greater the enzyme concentration, the greater the reaction rate.
T OR F?
T
Invertase (Classification: __________)
HYDROLASE
- hydrolyzes and breaks down the disaccharide Sucrose and polysaccharides molecules into its
monosaccharide forms of Glucose and Fructose. - e.g., Honey – a naturally inverted sugar;
supersaturated mixture of Fructose and Sucrose
INVERTASE
Sucrose does not dissolve fully at ______ temperature in water and as per its concentration, it will crystalize quickly
ROOM TEMP.
________ & ______ have a HIGHER SOLUBILITY IN WATER, so they do not crystallize after the inversion of sugar takes place (mixture is called inverted sugar through the process inversion - the optical property of the solution is changed from positive rotation to negative rotation
Fructose and Glucose
- a general test for compounds having a peptide bond
*_________ is a compound formed by HEATING UREA to 180° C, and when treated with dilute copper sulfate in alkaline condition, a PURPLE
colored compound is formed.
BIURET TEST
- a general test for ALL AMINO ACIDS
- due to a reaction between an amino group of free amino acid and Ninhydrin.
o Ninhydrin is a powerful oxidizing agent and its
presence, amino acid undergo oxidative deamination liberating ammonia, CO2, a corresponding aldehyde and reduced form of ninhydrin (hydrindantin).
o The NH3 formed from a amino group reacts with
another molecule of ninhydrin and is reduced
product (hydrindatin) to give a blue substance
(diketohydrin) - in some amino acids like proline and hydroxyproline, a different product having a bright yellow color is formed.
Asparagine: a brown colored product; has a free amide group
Ninhydrin Test
- used to detect amino acids containing an aromatic nucleus (tyrosine, tryptophan and phenylalanine) in a protein solution which gives YELLOW color nitro derivatives on
heating with conc. HNO3.
o the aromatic benzene ring undergoes nitration to give yellow colored product.
o Phenylalanine gives negative or weakly positive reaction though this amino acid contains an
aromatic nucleus because it is difficult to nitrate under normal conditions.
o On adding alkali to these nitro derivative salts,
the color changes from YELLOW TO ORANGE
Xanthoproteic Reaction
used to DETECT ALBUMIN (precipitate albumin using strong mineral acids
Tanret’s Test
- Copper sulfate (CuSO4)
- Sodium hydroxide
(NaOH) - Sodium potassium
tartrate (Rochelle Salt)
BIURET TEST REAGENTS
Ninhydrin solution
(Triketohydrindene hydrate)
NINHYDRIN TEST REAGENT
Nitric acid (HNO3)
* 40 % NaOH
XANTHOPROTEIC REACTION REAGENTS
Mercuric Chloride
* Potassium iodide
* Glacial acetic acid water
Tanret’s Test reagent
White precipitate
Tanret’s Test
A white precipitate forms on adding nitric acid which on heating dissolves and solution turns
YELLOW, upon adding alkaline the color changes to
ORANGE.
Xanthoproteic
Reaction
- Blue color/ Purplish with alpha amino acids
- Yellow color with amino acid Proline
NINHYDRIN TEST
appearance of purplish/violet color confirms the
presence of proteins
BIURET TEST
- states that when a solute ABSORBS LIGHT of a particular wavelength, the absorbance is DIRECTLY PROPORTIONAL to the CONCENTRATION of substance in a solution or INVERSELY PROPORTIONAL to the logarithm of the TRANSMITTED LIGHT
- most commonly used in protein assays (absorbance of light)
BEER’S LAW/BEER-LAMBERT LAW
BEER’S LAW states that:
The amount of absorbed light is proportional to solution concentration.
T or F?
T
