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CHM040 - BIOMOLECULES > Chapter 3: Protein Structure and Function > Flashcards

Chapter 3: Protein Structure and Function Flashcards

1
Q

Protein is derived from the greek wor ____ meaning ____

A

proteios means “first”

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2
Q

Why does the term protein derived from the Greek word proteios?

A

To indicate the central roles that proteins play in the living organisms

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3
Q

the indespensable agents of biological function

A

Proteins

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4
Q

building blocks of proteins

A

Amino acids

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5
Q

The stunning diversity of the thousands of proteins found in nature arises from the intrinsic properties of _ _ _ _ _ _

A

only 20 commonly occurring amino acids

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6
Q

These features include:

A
  1. the capacity to polymerize
  2. novel acid-base properties
  3. varied structure and chemical functionality in the amino acid side chains
  4. Chirality
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7
Q
  • or handedness
  • means that an object or molecule cannot be superimosed on its mirror image by any translation or rotations
A

Chirality

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8
Q

Classification of proteins

A

Structural
Contractile/Movement
Transport
Storage/Nutrient
Hormone/Regulatory
Enzyme
Protection/Defense

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9
Q
  • are biological catalysts
  • majority of this that have been studied are proteins
A

Enzymes

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10
Q

Function of Enzyme

A

Catalyze biochemical reactions in the cells

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11
Q

Examples of Enzyme

A
  • Sucrose
  • Trypsin
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12
Q

It catalyzes the hydrolysis of sucrose

A

Surcose

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13
Q

It catalyzes the hydrolysis of proteins

A

Trypsin

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14
Q

Example of the function of Enzymes

A

Digestive enzymes pepsin, trypsin, and chymotrypsin break down proteins in our diet so that subunits can be absorbed for use by our cells

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15
Q

Without _ , the body
cannot _ _

A
  • enzymes
  • absorb nutrients
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16
Q
  • it includes antibodies
  • specific protein molecules produced by specialized cells of the immune system in response to foreign antigens
A

Protection or Defense proteins

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17
Q

Antibodies also called as

A

Immunoglobulins

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18
Q

These foreign invaders include _ and _ that infect the body

A

bacteria and viruses

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19
Q

Each _ has regions that precisely fit and bind to a single _

A
  • each antibody
  • antigen
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20
Q

Antibody helps to end the ___ by _____ to the ______ and helping to _____ it or ______ it from the body.

A
  • infection
  • binding to the antigen
  • destroy
  • remove
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21
Q

Function of Protection/Defense Protein

A

Recognize and destroy foreign substances

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22
Q

Example of Protection/Defense Protein

A

Immunoglobulins

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23
Q

It stimulate immune responses

A

Immunoglobulins

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24
Q

carry materials from one place to
another in the body

A

Transport proteins

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25
Q

The protein that transports iron from the liver to the bone marrow

A

Transferrin

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26
Q

Transferrin is used to

A

it is used to synthesize the
heme group for hemoglobin

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27
Q

Transferrin is ______ and _______ into ____ mostly by the ___

A
  • synthesized and secreted
  • serum
  • liver
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28
Q

Synthesis of transferrin is regulated by _____

A

iron

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29
Q

Iron alone is _______ ______

A

extremely reactive

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30
Q

If iron is not bound by specific _____ ____ and/or _____ _____ within the body, it can _____ ____ with ____, _____, and _____ structures

A
  • serum carriers
  • storage proteins
  • viciously interact
  • vascular, cellular, and subcellular
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31
Q

Therefore, after absorption, it is bound to the _______ ____ _____ (TF) for ____ _____

A
  • plasma protein transferrin
  • safe transport
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32
Q

The proteins that are responsible for transport and storage of oxygen in higher organisms, respectively

A

Hemoglobin and myoglobin

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33
Q

Function of Transport proteins

A

carry essential substances throughout the body

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34
Q

Example of Transport proteins

A
  • Hemoglobin
  • Lipoproteins
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35
Q

transports oxygen

A

Hemoglobin

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36
Q

transport lipids

A

Lipoproteins

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37
Q

Structural Differences of Myoglobin and Hemoglobin:

Myoglobin

A
  • 1 subunit
  • heme group
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38
Q

Structural Differences of Myoglobin and Hemoglobin

Hemoglobin

A
  • 4 subunits
  • 4 hemegroups
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39
Q
  • it controls many aspects of cell function, inlcuding metabolism and reproduction
  • can only function within a limited set of conditions
A

Regulatory/Hormone proteins

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40
Q

Function of Regulatory/Hormone protein

A

Regulate body metabolism and the nervous system

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41
Q

In regulatory proteins, what must be carefully regulated for life to exist?

A
  • body temperature
  • the pH of the blood
  • blood glucose levels
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42
Q

Example of Regulatory/Hormone proteins

A
  • Insulin
  • Growth hormone
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43
Q

It regulates blood glucose level

A

Insulin

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44
Q

A hormone that regulate body function (proteins)

A

Insulin and Glucagon

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45
Q

The hormone that preps your body to cope with stress

A

Adrenaline: Fight or Flight

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46
Q

How your body creates Adrenaline cells?

A
  • eating high-protein foods,your liver extracts amino acids and sends them to the adrenal glands where they get reshaped into adrenaline and stores
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47
Q

How your body uses Adrenaline cells?

A

EMERGENCY
- your adrena glands release adrenaline into the blood in a “mass discharge”, your body shifts into “fight or flight” mode

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48
Q

Adrenaline: Fight or Flight
More blood travels to your brain:

A

Your mind is sharper

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49
Q

Adrenaline: Fight or Flight
Pupils dilate:

A

Your vision is clearer

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50
Q

Adrenaline: Fight or Flight
The airways in the lungs dilate:

A

Taking in more oxygen

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51
Q

Adrenaline: Fight or Flight
The hearts contracts more forcefully:

A

Pumps out more blood

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52
Q

Adrenaline: Fight or Flight
Sweat:

A

You sweat more

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53
Q

Adrenaline: Fight or Flight
The blood clots more readily:

A

Helps minimize blood loss

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54
Q

Adrenaline: Fight or Flight
The available source of fuel:

A

Blood levels of cholesterol, glucose and fatty acids, increases

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55
Q

Adrenaline: Fight or Flight
Skeletal muscles:

A

More blood gets more oxygen and glucose which strengthen the skeletal muscles

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56
Q

Adrenaline: Fight or Flight
Hunger is no longer a priority:

A

Blood vessels feeding the gastrointestinal tract narrow and digestive movements slow

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57
Q

How many minutes does these adrenalized effects last?

A

1 or 2 minutes

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58
Q

What happens to the adrenaline chamiclas after the threat passes?

A

The adrenaline chemicals oxidize and are converted into waste-product chemicals and are shipped out in urine

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59
Q

It provides mechanical support to large animals and provide them with their outer coverings

A

Structural proteins

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60
Q

Function of Structural proteins

A

Provide structural components

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61
Q

Example of Structural proteins

A
  • Collagen
  • Keratin
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62
Q

It is in tendons and cartilage

A

Collagen

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63
Q

It is in hair, skin, wool, and nails

A

Keratin

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64
Q

Which part of our body that are largely composed of the protein keratin?

A

Hair and fingernails

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65
Q

What is EB?

A

Epidermolysis bullosa

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66
Q

Babies that are born with EB are known as?

A

“butterfly babies”

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67
Q

People with EB have __ ___ resulting to ___ ____ ___ in the skin

A
  • genetic mutation
  • abnormal structural proteins
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68
Q

What is the effect of recessive Dystrophic EB?

A
  • difficulty to ingest food for a child
  • causes blistering that occurs in mouth, esophagus, and gastrointestinal tract
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69
Q

It is necessary for all forms of movement

A

Movement/Contractile proteins

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70
Q

Function of movement/contractile protein

A

Make muscles move, including the heart

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71
Q

Example of Movement/Contractile protein

A
  • Myosin
  • Actin
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72
Q

It contracts muscle fibers

A

Myosin and actin

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73
Q

It serve as sources of amino acids for embryos or infants

A

Nutrient proteins

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74
Q

Examples of Storage/Nutrient protein

A
  • Casein
  • Ferritin
  • Egg albumen
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75
Q

It stores protein in milk

A

Casein

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76
Q

It stores iron in the spleen and liver

A

Ferritin

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77
Q

these compounds contain both an amine and an acid

A

Amino acids

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78
Q

20 amino acids that are common in nature are all?

A

All 20 are α-amino acids

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79
Q

α (alpha) means

A

amine is adjacent to the carboxylate group

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80
Q

Out of all 20 amino acids, how many are stereoisomers?

A

19

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81
Q

What amino acid is not a stereoisomer out of all 20 common amino acid?

A

Glycine (does not have a chiral carbon)

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82
Q

The α-carbon of amino acids is ____

A

Chiral

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83
Q

What is a chiral molecule?

A

It is non-superposable to its mirror image due to the presence of an asymmetric carbon atom

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84
Q

Where does all the differences between amino acids depens upon?

A

side-chain R groups

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85
Q

Forming classes of Amino acids is based on, what?

A

Polarity of their side chains

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86
Q

Classes of Amino Acids

A
  • Nonpolar
  • Polar, neutral
  • Polar acidic
  • Polar basic
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87
Q

It is a class of amino acid that has hydrophobic R groups

A

Nonpolar

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88
Q

It is a class of amino acid that have a high affinity for water, but are not ionic at pH

A

Polar, neutral

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89
Q
  • it is a class of amino acid that have ionized carboxyl groups in their side chains
  • negatively charged
A

Polar acidic

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90
Q
  • are basic as the side chain reacts with water to release a hydroxide anion
  • positively charged
A

Polar basic

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91
Q

What are the amino acids that are essential for normal tissue growth and development?

A

All amino acids

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92
Q

What is the term that is reserved for those amino acids that must be supplied in the diet for proper growth and development?

A

“essential amino acids”

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93
Q

“PVT. TIM HALL”

A

Phe, Val, Thr, Trp, Ile, Met, His, Arg, Leu, Lys

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94
Q

___ and ___ are semi-essential; they not synthesized in sufficient quantities during infancy stage

A

His and Arg

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95
Q

α-carbon is attached to a:

A
  • Carboxyl group (̶ COOH)
  • Amino group ( ̶ NH2)
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96
Q

At physiologic pH the amino acid has:

A
  • Carboxyl group in –COO-
  • Amino group in –NH3+
  • Neutral molecule with equal number of + and – charges is called a zwitterion
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97
Q

What is a zwitterion?

A

Neutral molecule with equal number of + and – charges

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98
Q

From the German word “zwitter” which means

A

hybrid or hermaphrodite

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99
Q

Amino acids are __ ____ __ with __ ___ __ and __ ___ ___

A
  • white crystalline solids
  • high melting points
  • high water solubilities
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100
Q

What are the two charged groups?

A
  • basic amino group
  • carboxylic acid
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101
Q

The two charged groups at the two ends lead to

A

internal proton transfer, forming zwitterions

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102
Q

By changing the __ you can affect the __ ___ on the zwitterions

A
  • pH
  • net charge
103
Q

It is the pH point at which there is no net charge on the zwitterions

A

Isoelectric point (pI)

104
Q

What is the isoelectric point of an amino acid?

A

the pH at which it bears no net charge

105
Q

What is a form of acid that is more accurate depiction of its structure?

A

Zwitterionic

106
Q

A ____ contains two point charges but is ___ overall

A
  • zwitterion
  • neutral
107
Q

At pH values below isoelectric point

A

bear net positive charge

108
Q

At pH above isoelectric point

A

bear net negative charge

109
Q

It is a test by applying a sample of the amino acid to specially treated paper or gel and applying an electric field at different pH values

A

Electrophoresis

110
Q

A molecule with a net charge of zero will __ migrate in an electric field

111
Q

positive charge (+) will migrate toward

A

cathode (-)

112
Q

negative charge (-) will migrate toward

113
Q

For a typical amino acid with a neutral sidechain R:

A
  • the positively charged form (+1) dominates at low pH
  • the zwitterionic (neutral) form dominates at intermedaite pH
  • the negatively charged form (-1) dominates at high pH
114
Q

For an amino acid with an acidic sidechain:

A
  • the positively chargde form (+1) dominates very low pH
  • the zwitterionic (neutral) form dominates at low pH
  • the negatively charged form (-1) dominates at intermediate pH
  • at strong basic pH a doubly negatively charged form (-2) may form
115
Q

For an amino acid with a basic sidechain (e.g. lysine)

A
  • the doubly positive charged form (+2) dominates at very low pH
  • the positively charged form (+1) dominates at intermediate pH
  • the zwitterionic form (neutral) forms at basic pH
  • at strongly basic pH, the negatively charged form (-1) dominates
116
Q

What is the pI values of the polar acidic amino acids?

117
Q

What are the polar acidic amino acids?

A
  • Aspartic acid
  • Glutamic acid
118
Q

The carboxylic acid in R groups of their zwitterions at pH 3 is __ ___

A

Not ionized

119
Q

The carboxylic acid in R groups at physiological pH __ _ to form a ___ ___ `

A
  • loses H+
  • negatively charged
120
Q

What is the pI values of basic amino acids?`

A

typically higher than physiological pH value, ranging from pH 7.6 to 10.8

121
Q

The amines in the R groups of the basic amino acids at physiological pH values __ _ to form an ___ ___ __

A
  • gain H+
  • overall positive charge
122
Q

What are the basic amino acids?

A
  • lysine
  • arginine
  • histidine
123
Q

Amino acid:
Neutral

A

Isoelectric pH:
4.8 - 6.3

124
Q

Example of Neutal Amino Acid

125
Q

Amino acid:
Acidic

A

Isoelectric pH:
2.8 - 3.2

126
Q

Example of Acidic Amino Acid

127
Q

Amino acid:
Basic

A

Isoelectric pH:
7.8 - 10.8

128
Q

Example of Basic Amino Acid

129
Q

It is an analytical method for identifying amino acids by observing their migration as a function of pH under an applied electric field gradient

A

Electrophoresis

130
Q

If an amino acid carries a positive charge at pH<pI, it will ___

A

migrate to the negative electrode (cathode)

131
Q

If an amino acid carries a negative charge at pH>pI, it will ___

A

migrate to the positive charge electrode (anode)

132
Q

What are the techniques in separating amino acids?

A
  1. Ion-exchange chromatography
  2. Size-exclusion chromatography
  3. Affinity chromatography
133
Q

Ion-excahnge chromatography

A

Separates the compounds base on charge

134
Q

Size-exclusion chromatography

A

Separates compounds base on size

135
Q

Affinity chromatography

A

Separates the compounds base on the interaction between the protein of interest and ligand

136
Q

A result of covalent bonding between the amino acids

A

The Peptide Bonds

137
Q

In peptide bonds, proteins are?

A

linear polymers of L-α-amino acids

138
Q

The peptide bond:
Carboxyl group of one amino acid is linked to ___

A

the amino group of another amino acid

139
Q

It is an amide bond or peptide linkage

140
Q

What is the reaction involve in peptide bond?

A

Dehydration reaction

141
Q

What is produce if the two amino acids are condensed or dehydrated?

142
Q

N-terminal amino acid

A

Amino acid with a free a-NH3+ group

143
Q

C-terminal amino acid

A

Amino acid with a free –COO ̶ group

144
Q

Amino acid structures are written with the ___

A

N-terminal on the left

145
Q

amino acids are polymerized into ___ and ___

A

peptides and proteins

146
Q

It is used for molecules composed over 50 amino acids

147
Q

It is used for molecules of less than 50 amino acids

148
Q

Naming Peptides

A
  • The far right AA residue retains the name of the amino acid
  • All AAs (except TRYPTOPHAN) → - ine or –ic acid is replaced by –yl
  • Tryptophan becomes tryptophanyl
149
Q

Small Peptides

A
  1. Aspartame (Asp-Phe)
  2. Glutathione (Glu-Cys-Gly)
  3. Enkephalins (Tyr-Gly-Gly-Phe-Leu & Tyr-Gly-Gly-Phe-Met)
  4. Oxytocin (Ile-Leu)
  5. Vasopressin (Phe-Arg)
150
Q
  • it is the artificial sweetener used in almost every diet food on the market today
  • its caloric content is the same as sucrose but is ~180 times as sweet
A

Aspartame (Asp-Phe)

151
Q

Forms have a bitter taste

A
  • L-D
  • D-L
  • D-D
152
Q
  • it functions as an antioxidant, protecting cellular contents from oxidizing agents such as peroxides and superoxides
A

Glutathione (Glu-Cys-Gly)

153
Q

What are the oxidizing agents that are highly reactive forms of oxygen often generated within a cell?

A

Peroxides and Superoxides

154
Q

Glu is bonded to Cys through the ___ ___ ___ rather than through the ___ ____ ___

A
  • side-chain carboxyl group
  • α-carbon carboxyl group
155
Q
  • natural painkillers produced in the body
  • it is bind to receptors in the brain to give relief from pain
A

Enkephalins and Endorphins

156
Q
  • it is the first hormone to be synthesized in the laboratory
  • a nonpeptide used to initiate labor
157
Q

Oxytocin stimulates ____ _____ in labor

A

uterine contractions

158
Q
  • an antidiuretic hormone
  • regulates blood pressure by adjusting the amount of water reabsorbed by the kidneys
A

Vasopressin

159
Q
  • partly responsible for triggering pain, welt formation (as in scratches), movement of smooth muscle, and lowering of blood pressure
A

Bradykinin (Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg)

160
Q

completely inactive, hence, the name bogus or false

A

Boguskinin (Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe- )

161
Q

Val-His-Leu-Thr-Pro-Glu-Glu-Lys-Ser-Ala-

162
Q

Val-His-Leu-Thr-Pro-Val-Glu-Lys-Ser-Ala-

A

Sickle-cell Hb

163
Q

Val-His-Leu-Thr-Pro-Glu-Lys-Lys-Ser-Ala-

A

Georgetown anemia

164
Q

The sickled cells are unable to pass through the ___ _____ of the circulatory system, and circulation is ____

A
  • small capilliaries
  • hindered
165
Q

Effect of sickled cells in human body

A
  • damage to many organs (bone and kidney)
  • can lead to death at an early age
166
Q

It is results from formation of covalent peptide bonds between amino acids

A

Primary Structure of Proteins

167
Q

What is the Primary Structure of Proteins?

A

The amino acid sequence of the polypeptide chain

168
Q

The peptide bond has a __ ___ __ character

A

partial double bond

169
Q

There is __ ___ around __ __ of the three single bonds of a peptide backbone

A
  • free rotation
  • only two
170
Q

R groups on adjacent amino acids are on ____ ___ of the chain because of the rigid peptide bond.

A

Opposite sides

171
Q

How does the Second Structure of Proteins is formed?

A

When the primary sequence of the polypeptide folds into regularly repeating structures

172
Q

Secondary structure results from ___ ___ between the _____ ___ and ______ ___ of the peptide bonds

A
  • hydrogen bonding
  • amide hydrogens (N—H)
  • carbonyl oxygens (C=O)
173
Q

Most common type of secondary structure

A
  • Coiled
  • Helical
174
Q

Secondary Sructure of Proteins includes:

A

α-helix and β-sheet

175
Q

Important features of Secondary Structure of Proteins: α-Helix

A
  • Each amide H and carbonyl O is involved in H bonds locking the helix in place
  • Carbonyl O links to amide H 4 amino acids away
  • H bonds are parallel to the long axis of the helix
  • Helix is right-handed
  • Repeat distance or pitch is 5.4 angstroms
  • 3.6 amino acids per turn
176
Q

In α-Helix, the borken line represents the? (tanawa lng nnyo sa pdf na gi send ni maam ang picture hehe sankss)

A

Hydrogen bonds

177
Q

What is the direction Hydrogen bonds in α-Helix?

A

Parallel to the direction of the helix

178
Q

are arranged in a secondary structure of fibers or sheets with only 1 type of secondary structure

A

Fibrous proteins

179
Q
  • it is the second most common secondary structure
  • appears similar to folds of fabric
A

β-pleated sheet

180
Q

In β-pleated sheet, what organic compounds that are involved in the H bonds with the chain nearly completely extended?

A
  • carbonyl O
  • amide H
181
Q

β-pleated sheet:
Two possible orientation

A
  1. Parallel
  2. Antiparallel
182
Q

Two possible orientation:
Parallel

A

The N-termini are head-to-head

183
Q

Two possible orientation:
Antiparallel

A

The N-terminus of one chain is aligned with the C-terminus of the other

184
Q
  • three-dimensional structure
  • overall folding of the entire polypeptide chain
  • defines the biological function of proteins
A

The Tertiary Structure of Proteins

185
Q
  • forms spontaneously
  • maintained by interactions among the side chains or R groups
A

Globular tertiary structure

186
Q

Types of Interactions Maintaining Tertiary Structure

A
  1. Disulfide bridges
  2. Salt bridges
  3. Hydrogen bonds
  4. Hydrophobic interactions
187
Q

Disulfide bridges

A

interaction between two cysteine residue

188
Q

Linkage that occurs within the same chain

A

Intrachain

189
Q

Linkage the occurs between 2 or more chains

A

Interchain

190
Q

Salt bridges

A
  • ionic interaction/electrostatic attraction
  • interaction between ionic side chains –COO– and –NH3+
191
Q

Hydrogen bonds

A

Interaction between polar residue side chains

192
Q

Hydrophobic interactions

A

two nonpolar groups are attracted by a mutual repulsion of water

193
Q
  • it is the arrangement of subunits or peptides that form a larger protein
  • is maintained by the same forces which are active in maintaining tertiary structure
A

The Quaternary Structure of Proteins

194
Q

What is the functional form of many proteins?

A

Aggregate of several globular peptides

195
Q

A polypeptide chain having primary, secondary, and tertiary structural features that is a part of a larger protein

196
Q

Protein Functions Follow Shape
Fibrous proteins:

A
  • Mechanical strength
  • Structural components
  • Movement
197
Q

Protein Functions Follow Shape
Globular proteins:

A
  • Transport
  • Regulatory
  • Enzymes
198
Q

Shape of Globular proteins

A

Roughly circular

199
Q

Shape of Fibrious proteins

A

Long strands

200
Q

Amino acid sequence of Globular proteins

A

Irregular and wide range of R groups

201
Q

Amino acid sequence of Fibrious proteins

A

Repetitive with a limited range of R groups

202
Q

Function of Globular proteins

A

Physiological/functional

203
Q

Function of Fibrious proteins

A

Structural

204
Q

Examples of Globular proteins

A
  • Hemoglobin
  • Enzymes
  • Insulin
  • Immunoglobulin
205
Q

Examples of Fibrous proteins

A
  • Collagen
  • Keratin
  • Myosin
  • Actin
  • Fibrin
206
Q

Solubility of Globular proteins

A

(generally) soluble in water

207
Q

Solubility of Fibrous proteins

A

(generally) insoluble in water

208
Q

Hemoglobin in Normal (wild-type)

A

Normal (Globular)

209
Q

Red Blood Cell in Normal (wild-type) Hemoglobin

A

Round (biconcave)

210
Q

Blood Vessels in Normal (wild-type) Haemoglobin

A

Free flowing

211
Q

Hemoglobin in ‘Sickle Cell’

A

Clumped (fibrous)

212
Q

Red Blood Cell in ‘Sickle Cell’ Hemoglobin

A

Sickle-shaped

213
Q

Blood Vessels in ‘Sickle Cell’ Hemoglobin

A

Forms clots/blockages

214
Q

It is a protein to which another chemical group (e.g., carbohydrate) is attached by either covalent bonding or other interactions

A

Conjugated Proteins

215
Q

It is the oxygen storage protein of skeletal muscle

216
Q

It is the oxygen-transport protein of higher animals

A

Hemoglobin

217
Q

Why does the oxygen is transferred from hemoglobin to myoglobin?

A

Since the myoglobin has a stronger attraction for oxygen than hemoglobin does

218
Q

It is an essential component of the proteins hemoglobin and myoglobin

A

Heme group

219
Q

In the heme group, it is the oxygen binding site

A

Fe2+, ferous ion

220
Q

Each hemoglobin contains a ___ ___ which can hold __ ____ of oxygen (O2)

A
  • heme group
  • 1 molecule
221
Q

Hemoglobon
T-form:

A
  • taut or tense
  • Deoxy: low O2 affinity
222
Q

Hemoglobon
R-form:

A
  • relaxed
  • Oxy: high O2 affinity
223
Q

The disruption of bonds in the secondary, tertiary, and quaternary protein structures

A

Protein Denaturation

224
Q

It is the loss of organized structure of a globular protein

A

Denaturation

225
Q

It is the breaking of bonds using water

A

Hydrolysis

226
Q
  • splits the peptide bonds to give smaller peptides and amino acids occurs in the digestion of proteins
  • occurs in cells when amino acids are needed to synthesize new proteins and repair tissues
A

Protein Hydrolysis

227
Q

In the lab, the hydrolysis of a peptide requires __ or ___, ___, and ___

A

acid or base, water, and heat

228
Q

In the body, _____ catalyze the hydrolysis of proteins

229
Q

Some practical aspects of protein denaturation

A
  1. Heat and UV
  2. Salts of heavy metal ions esp. Hg2+, Pb2+, Ag+
  3. Organic compounds such as soap, detergents, phenol, and aliphatic alcohol
230
Q

Protein Sequencing
Steps in determining the amino acid sequence:

A
  1. hydrolysis - by acid, alkali, or enzyme
  2. identification of the products of hydrolysis
  3. fitting the pieces together as you would a jigsaw puzzle
231
Q

Protein Sequencing
HYDROLYSIS

A
  1. Acid Hydrolysis
  2. Alkali Hydrolysis
  3. Cyanogen bromide
  4. Enzymatic Hydrolysis by proteases/ peptidases
232
Q
  • involves heating in the presence of 6N HCl
  • the protein is completely hydrolyzed, but Trp, is destroyed completely and Ser, Thr, and Tyr are partially destroyed
A

Acid Hydrolysis

233
Q
  • heating in the presence of 4N NaOH
  • does not damage Trp, but destroys Arg, Cys, Thr, & Ser; and some amino acids are partly deaminated
  • more disadvantageous
  • it is used in quantitative determination of this amino acid
A

Alkali Hydrolysis

234
Q
  • cuts peptide bonds on the carboxylterminal side of methionine residues
  • used to reduce the size of polypeptide segments for identification and sequencing
A

Cyanogen bromide

235
Q

Two types of Enzymatic Hydrolysis

A
  1. Exopeptidases
  2. Endopeptidases
236
Q

Enzymes that cleave external peptide bonds

A

Exopeptidases

237
Q

Exopeptidases is used in __

A

the determination of the amino
acid sequence of peptides

238
Q

Enzymes under Exopeptidases

A
  1. Aminopeptidases
  2. Carboxypeptidases
239
Q

It sequentially cleaves peptide bonds, beginning at the N-terminal end of the polypeptide

A

Aminopeptidases

240
Q

It sequentially cleaves peptide bonds beginning at the C-terminal end of the polypeptide

A

Carboxypeptidases

241
Q

Enzymes that cleave internal peptide bonds

A

Endopeptidases

242
Q

Enzymes under Endopeptidases

A
  1. Trypsin
  2. Chymotrypsin
  3. Elastase
  4. Pepsin
  5. Thermolysin
243
Q

It cleaves peptide bonds at the carboxyl end of the two strongly basic amino acids: arginine and lysine

244
Q

It cleaves peptide bonds at the carboxyl end of the three aromatic amino acids: phenylalanine, tyrosine, & trptophan; and Leucine

A

Chymotrypsin

245
Q

It cleaves on the carboxyl side of Gly and Ala

246
Q

It cleaves peptide bonds at the amino end of the three aromatic amino acids: phenylalanine, tyrosine, tryptophan; acidic amino acids, Asp and Glu; and Ile

247
Q

It cleaves peptide bonds at the amino end of the three aromatic amino acids, Phe, Tyr, Trp; and amino acids with bulky nonpolar R groups, Leu, Ile, and Val

A

Thermolysin

248
Q

Other methods for determining the N-terminal end (chemical method)

A
  1. Sanger’s Method
  2. Edman Degradation
249
Q

The key reagent in this method for identifying the N-terminus is 1-fluoro-2,4-dinitrobenzene

A

Sanger’s Method

250
Q
  • can be done sequentially one residue at a time on the same sample
  • usually, one can determine the first 20 or so amino acids from the N-terminus by this method
A

Edman Degradation

251
Q

What is the key reagent in the
Edman degradation?

A

phenyl isothiocyanate

252
Q

Other methods for determining the C-terminal end (chemical method)

A

Hydrazine Method

253
Q

Hydrazine reacts with all amino acids whose carboxyl group is bound in peptide linkage, creating ____ ____ ____

A

Amino acyl hydrazides

254
Q

It regulates body growth

A

Growth hormones

CHM040 - BIOMOLECULES (4 decks)

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