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BIOCHEM LAB > PRE FI: STRUCTURAL ORGANIZATIONS OF PROTEINS > Flashcards

PRE FI: STRUCTURAL ORGANIZATIONS OF PROTEINS Flashcards

1
Q
  • linear sequence of amino acids
  • it determines the identity of protein, molecular
    structure, function and binding capacity
A

PRIMARY STRUCTURE

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2
Q
  • Arrangement of atoms of backbone in space.
  • local interactions between stretches of a polypeptide
    chain and includes α-helix and β-pleated sheet
    structures
A

SECONDARY STRUCTURE

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3
Q
  • 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.
A

Tertiary Structure

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4
Q
  • 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
A

Quaternary Structure

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5
Q

Proteins with quaternary structure are often referred to as ______________

A

OLIGOMERIC PROTEINS

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6
Q
  • 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
A

PROTEIN DENATURATION

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7
Q

ESSENTIAL AMINO ACIDS

A
  1. HISTIDINE
  2. ISOLEUCINE
  3. LEUCINE
  4. METHIONINE
  5. PHENYLALANINE
  6. THREONINE
  7. TRYPTOPHAN
  8. VALINE
  9. LYSINE
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8
Q

CONDITIONALLY NON-ESSENTIAL AMINO ACIDS

A
  1. ARGININE
  2. ASPARAGINE
  3. GLUTAMINE
  4. GLYCINE
  5. PROLINE
  6. SERINE
  7. TYROSINE
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9
Q

NON - ESSENTIAL AMINO ACIDS

A
  1. ALAMINE
  2. ASPARTATE
  3. CYSTEINE
  4. GLUTAMATE
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10
Q

Required for growth in children and is not essential for adults (only considered essential when a person is ill or stressed)

A

Conditionally Non-Essential Amino Acids

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11
Q

21st Amino Acid:

A

Selenocysteine/SEC

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12
Q

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

A

Sulfur/sulfhydryl group

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13
Q

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

A

Aromatic group

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14
Q

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

A

Imidazole ring

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15
Q

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

A

Guanidine group

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16
Q

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

A

Indole group

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17
Q

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

A

Storage proteins

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18
Q

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

A

Structural proteins

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19
Q

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

A

Messenger proteins

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20
Q

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

A

Transport proteins

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21
Q

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

A

Respiratory pigments

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22
Q
  • 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
A

ENZYMES

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23
Q

ENZYMES LOWER THE ACTIVATION ENERGY OF
CHEMICAL REACTIONS.

TRUE OR FALSE?

A

TRUE

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24
Q

the amount of energy that must be put in for the reaction to begin

A

ACTIVATION ENERGY

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25
Q

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.

A

OXIDOREDUCTASES

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26
Q

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

A

TRANSFERASES

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27
Q

SUBTYPE OF TRANSFERASE
- catalyze transfer of an AMINO group to a substrate

A

TRANSAMINASES

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28
Q

SUBTYPE OF TRANSFERASE
- catalyze transfer of a PHOSPHATE group from
adenosine triphosphate (ATP) to a substrate

A

KINASES

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29
Q

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

A

HYDROLASES

30
Q

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)

A

LYASES

31
Q

LYASES
- effects the REMOVAL of the components of water from a double bond

A

Dehydratase

32
Q

LYASES
- effects the ADDITION of the components of water to a double bonds

A

Hydratase

33
Q

ENZYME CLASSIFICATION
* catalyze the ISOMERIZATION (REARRANGEMENT OF ATOMS) of a substrate in a reaction, converting it into a molecule isomeric with itself.

A

ISOMERASES

34
Q

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

A

LIGASE

35
Q

a measure of the rate at which enzyme converts substrate to products in a biochemical reaction

A

ENZYME ACTIVITY

36
Q

FACTORS AFFECTING ENZYME ACTIVITY

A
  1. TEMPERATURE
  2. pH
  3. SUBSTRATE CONCENTRATION
  4. ENZYME CONCENTRATION
37
Q

Higher temperature = higher kinetic energy = increase in number of reactant collisions, therefore there is higher activity

TRUE OR FALSE?

A

TRUE

38
Q

temperature at which the rate of enzyme catalyzed reaction is maximum

A

Optimum temperature

39
Q

Optimum temperature for human enzymes is

A

37ºC (body temperature)

40
Q

Increased temperature (high fever) leads to

A

decreased enzyme activity

41
Q

Drastic changes in pH can result in denaturation of
proteins

TRUE OR FALSE?

A

TRUE

42
Q

pH at which enzyme has maximum activity

A

Optimum pH

43
Q

Most enzymes have optimal activity in the pH range
of

A

7.0 - 7.5

44
Q

Most enzymes have optimal activity in the pH range
of 7.0 - 7.5
o Exception:

A

DIGESTIVE ENZYMES LIKE PEPSIN AND TRYPSIN

45
Q

Pepsin: Optimum pH =

A

2.0

46
Q

Trypsin: Optimum pH =

A

8.0

47
Q

at a CONSTANT enzyme concentration, the enzyme activity increases with increased substrate concentration

TRUE OR FALSE

A

TRUE

48
Q

the concentration at which it reaches its MAXIMUM RATE and all of the ACTIVE SITES ARE FULL

A

Substrate saturation

49
Q

Number of SUBSTRATE MOLECULES converted to PRODUCT PER SECOND PER ENZYME molecule under conditions of optimum temperature and
pH

A

Turnover Number

50
Q

Enzymes are consumed in the reactions they
catalyze

TRUE OR FALSE?

A

FALSE, THEY ARE NOT CONSUMED

51
Q

at a CONSTANT substrate concentration, enzyme activity increases with increase in enzyme concentration

TRUE OR FALSE?

A

TRUE

52
Q

the greater the enzyme concentration, the greater the reaction rate.

T OR F?

A

T

53
Q

Invertase (Classification: __________)

A

HYDROLASE

54
Q
  • 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
A

INVERTASE

55
Q

Sucrose does not dissolve fully at ______ temperature in water and as per its concentration, it will crystalize quickly

A

ROOM TEMP.

56
Q

________ & ______ 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

A

Fructose and Glucose

57
Q
  • 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.
A

BIURET TEST

58
Q
  • 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
A

Ninhydrin Test

59
Q
  • 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
A

Xanthoproteic Reaction

60
Q

used to DETECT ALBUMIN (precipitate albumin using strong mineral acids

A

Tanret’s Test

61
Q
  • Copper sulfate (CuSO4)
  • Sodium hydroxide
    (NaOH)
  • Sodium potassium
    tartrate (Rochelle Salt)
A

BIURET TEST REAGENTS

62
Q

Ninhydrin solution
(Triketohydrindene hydrate)

A

NINHYDRIN TEST REAGENT

63
Q

Nitric acid (HNO3)
* 40 % NaOH

A

XANTHOPROTEIC REACTION REAGENTS

64
Q

Mercuric Chloride
* Potassium iodide
* Glacial acetic acid water

A

Tanret’s Test reagent

65
Q

White precipitate

A

Tanret’s Test

66
Q

A white precipitate forms on adding nitric acid which on heating dissolves and solution turns
YELLOW, upon adding alkaline the color changes to
ORANGE.

A

Xanthoproteic
Reaction

67
Q
  • Blue color/ Purplish with alpha amino acids
  • Yellow color with amino acid Proline
A

NINHYDRIN TEST

68
Q

appearance of purplish/violet color confirms the
presence of proteins

A

BIURET TEST

69
Q
  • 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)
A

BEER’S LAW/BEER-LAMBERT LAW

70
Q

BEER’S LAW states that:
The amount of absorbed light is proportional to solution concentration.

T or F?

A

T

BIOCHEM LAB (8 decks)

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