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Biomolecules CHM040 > Chapter 3: Proteins and Amino Acids > Flashcards

Chapter 3: Proteins and Amino Acids Flashcards

1
Q

the building blocks of proteins

A

amino acids

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2
Q

indispensable agents of biological function

A

proteins

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3
Q

how many naturally ocurring amino acids are there?

A

20

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4
Q

features of amino acids (4)

A

(1) the capacity to polymerize
(2) novel acid–base properties
(3) varied structure and chemical functionality in the amino acid side chains, and
(4) Chirality (or handedness, means that an object or molecule cannot be superimposed on its mirror image by any translations or rotations)

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5
Q

Classes of Protein (7)

A
  • Structural
  • Contractile
  • transport
  • storage
  • hormone
  • enzyme
  • protection
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6
Q

Class of Protein: Provide structural components.
Give examples and their function

A

STRUCTURE
Collagen is in tendons and cartilage
Keratin is in hair, skin, wool, and nails.

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7
Q

Class of protein: Move muscles.
Give examples and their function

A

CONTRACTILE
Myosin and Actin contract muscle fibers.

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8
Q

Class of protein: Carry essential substances throughout the body.
Give examples and their function

A

TRANSPORT
Hemoglobin transports oxygen.
Lipoproteins transport lipids.

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9
Q

Class of protein: Store nutrients.
Give examples and their function

A

STORAGE
Casein stores protein in milk.
Ferritin stores iron in the spleen and liver.

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10
Q

Class of protein: Regulate body metabolism and nervous system.
Give examples and their function

A

HORMONE
Insulin regulates blood glucose levels.
Growth hormone regulates body growth.

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11
Q

Class of protein: Catalyze biochemical reactions in the cells.
Give examples and their function

A

ENZYME
Sucrase catalyses the hydrolysis of sucrose.
Trypsin catalyzes the hydrolysis of proteins. (aids with digestion)

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12
Q

Class of protein: Recognize and destroy foreign substances.
Give an example and its function

A

PROTECTION
Immunoglobulins stimulate immune responses

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13
Q

biological catalysts

A

enzymes

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14
Q

Examples of enzymes that break down proteins in our diet so that subunits can be absorbed for use by our cells.

A

digestive enzymes:
- pepsin
- trypsin
- chymotrypsin

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15
Q

Without _, the body cannot absorb nutrients.

A

enzymes

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16
Q

Defense proteins include __
(also called __) which are specific protein molecules produced by specialized cells of the __ in response to __.
These foreign invaders include __
and __ that infect the body. Each
antibody has regions that precisely fit and bind to a single __. It helps to end the infection by __ and helping to destroy it or remove it from the body.

A
  • antibodies
  • immunoglobulins
  • immune system
  • foreign antigens
  • bacteria; viruses
  • antigen
  • binding to the antigen
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17
Q

How do defense proteins work in the body?

A
  1. Antibodies coat free virus particles. The virus envelope cannot fuse with the host cell membrane.
  2. The antibody-coated virus is recognized and phagocytosed by a macrophage.
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18
Q

Proteins that carry materials from one place to another in the body.

A

transport proteins

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19
Q

What is transferrin and its function in the body?

A
  • Transferrin is synthesized and secreted into serum mostly by the liver. Synthesis of transferrin is regulated by iron.
  • transports iron from the liver to the bone marrow, where it is used to synthesize the heme group for hemoglobin.
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20
Q

Transferrin: Iron alone is extremely reactive. If iron is not bound by __ and/or __ within the body, it can viciously interact with __, __, and __structures. Therefore, after absorption, it is bound to the __ for safe transport.

A
  • specific serum carriers
  • storage proteins
  • vascular; cellular; subcellular
  • plasma protein transferrin (TF)
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21
Q

Iron uptake from transferrin involves the __ to the transferrin receptor, __of transferrin within an __ by receptor-mediated endocytosis, and __ from the protein by decreasing endosomal pH (4.0-6.5). A reduction in pH induces the __ from transferrin in a process that involves a conformational change in the protein from a closed to an open form due to __

A
  • transferrin binding
  • internalization
  • endocytic vesicle
  • iron release
  • release of iron
  • pH change
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22
Q

Transport proteins: Explain the regulation of iron uptake by cells

A
  1. Holo-transferrin refers to transferrin that is bound to iron on the cell surface. Holo-transferrin is the form of transferrin that carries iron to cells for their iron requirements.
  2. Internalization: This step involves the internalization of iron-bound transferrin (holo-transferrin) into the cell. This is typically accomplished through receptor-mediated endocytosis.
  3. Apo-transferrin refers to transferrin that is not bound to iron. After holo-transferrin delivers iron to the cells, it becomes apo-transferrin. Apo-transferrin is then released from the transferrin receptor.
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23
Q

responsible for the transport and storage of oxygen in higher organisms

A

hemoglobin and myoglobin

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24
Q

difference between hemoglobin and myoglobin (function and structure)

A
  • Hemoglobin is a heterotetrameric oxygen transport protein found in red blood cells (erythrocytes).
    Hemoglobin is made up of four heme groups that are in each of hemoglobin’s four subunits.
  • Myoglobin is a monomeric protein found mainly in muscle tissue where it serves as an intracellular storage site for oxygen.
    Myoglobin is made up of one heme group in its 1 subunit.
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25
Q

Aspects in the body that must be regulated for life to exist

A
  • body temperature
  • pH of the blood
  • blood glucose levels
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26
Q

control many aspects of cell function, including metabolism and reproduction.

A

regulatory proteins

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27
Q

Insulin and glucagon relationship (role)

A

Glucagon increases blood sugar levels, whereas insulin decreases blood sugar levels.

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28
Q

Insulin and glucagon differentiation (definition, function)

A
  • insulin is a hormone produced by beta cells in the pancreas. Its primary role is to lower blood glucose levels by facilitating the uptake of glucose by cells, promoting its storage in the form of glycogen, and inhibiting the release of glucose from the liver.
  • Glucagon is a hormone produced by alpha cells in the pancreas, specifically in the islets of Langerhans. It plays a vital role in regulating blood glucose levels. Glucagon has the opposite effect of insulin, which is produced by beta cells in the pancreas.
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29
Q

What is adrenaline?

A

Adrenaline, also known as epinephrine, is a hormone and neurotransmitter that plays a crucial role in the body’s “fight or flight” response. It is produced by the adrenal glands, which are located on top of each kidney.

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30
Q

physiological effects of adrenaline

A
  • heart contracts more forcefully and pumps more blood
  • increase of available sources of fuel (blood levels of cholesterol, glucose, fatty acids)
  • airways of the lungs dilate; more oxygen
  • dilated pupil; clearer vision
  • sweat more
  • more blood travels to the brain; sharper mind
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31
Q

adrenalized effects last for

A

1-2 minutes

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32
Q

What happens when adrenaline is done with its job?

A

Adrenaline chemicals oxidize, converted into waste products. The body gets rid by mixing them with urine

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33
Q

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

A

structural proteins

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34
Q

Our hair and fingernails are largely composed of the protein __. Other structural proteins provide mechanical strength for our __, __, and __. Without such support, large, multicellular organisms like ourselves could not exist

A
  • keratin
  • bones
  • tendons
  • skin
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35
Q

a rare genetic disorder that affects the skin and mucous membranes. It is often referred to as the “butterfly disease” because individuals with this condition have extremely fragile skin that can blister or tear with minimal friction or pressure. The term “__” is a nickname for people, particularly children, with EB due to the delicate and sensitive nature of their skin.

A
  • Epidermolysis bullosa
  • “butterfly babies”
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36
Q

__ is the most severe, chronic type of EB. Blistering begins at __ or __. Much of the skin is covered in blisters and there is extensive __. Children can develop deformities caused by the recurrent scarring of the fingers and toes (__) and the hands and arms become fixed in stiff positions (__). It is painfully difficult for a child with this to __ due to the internal blistering that occurs in the __, __, and __.

A
  • Recessive Dystrophic EB
  • birth; shortly afterward
  • internal blistering
  • pseudosyndactyly
  • contractures
  • ingest food
  • mouth, esophagus, and gastrointestinal tract
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37
Q

proteins found in muscle cells. They play a crucial role in muscle contraction.
1. a thick filament
2. a thin filament

A
  1. myosin
  2. actin
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38
Q

These are byproducts of a chemical reaction that occurs when myosin interacts with actin. What’s their role in the context of muscle contraction?

A

Pi (inorganic phosphate)
ADP (adenosine diphosphate)

  • Pi and ADP dissociate from myosin after they have been used in the process of muscle contraction.
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39
Q

In muscle contraction, explain ATP binding and ATP hydrolysis

A
  • During muscle contraction, ATP binds to myosin, providing the energy needed for myosin to detach from actin.
  • After ATP binds to myosin, it is hydrolyzed, meaning it loses one of its phosphate groups, becoming ADP and inorganic phosphate (Pi). This release of energy from ATP hydrolysis powers the movement of myosin and the sliding of actin filaments, allowing muscle contraction to occur.
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40
Q

How do calcium ions (Ca²⁺) play a crucial role in muscle contraction?

A

When a nerve signal triggers a muscle to contract, it leads to the release of calcium ions from storage sites within the muscle cell. Calcium ions then bind to specific sites on actin, allowing myosin to interact with actin and initiate the sliding of filaments.

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41
Q

serve as sources of amino acids for embryos or infants.
Give examples

A

Nutrient protein
nutrient storage proteins: Egg albumen and casein in milk

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42
Q

a type of protein found in milk and dairy products. It is the primary protein component of cow’s milk, accounting for about 80% of the total protein content.

A

casein

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43
Q

often simply referred to as egg white, is the clear liquid portion of an egg that surrounds the yolk. It is primarily composed of water and protein and serves various culinary and nutritional purposes.

A

egg albumen

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44
Q

What is the characteristic feature of compounds known as amino acids?

A

Amino acids contain both an amine group and an acid group.

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45
Q

How many amino acids are common in nature?

A

Out of hundreds of amino acids that can be formed, only 20 are common in nature.

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46
Q

What is the special property of all 20 common amino acids?

A

All 20 common amino acids are α-amino acids, where “α” indicates that the amine group is adjacent to the carboxylate group.

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47
Q

How many out of the 20 common amino acids are stereoisomers?

A

Nineteen out of the 20 common amino acids are stereoisomers. Glycine is an exception because it does not have a chiral carbon.

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48
Q

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

A

chiral molecule (α-carbon in amino acid)

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49
Q

What is the primary basis for the differences between amino acids?

A

The differences between amino acids depend upon their side-chain R groups.

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50
Q

How are amino acids classified? What are the classes of amino acids?

A
  • based on the polarity of their side chains
  • Amino acids are classified into nonpolar, polar neutral, polar acidic (negatively charged), and polar basic (positively charged) classes based on the polarity of their side chains.
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51
Q

What characterizes the nonpolar class of amino acids?

A

The nonpolar class of amino acids has hydrophobic R groups.

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52
Q

What are the characteristics of amino acids in the polar neutral class?

A

Amino acids in the polar neutral class have a high affinity for water but are not ionic at a neutral pH.

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53
Q

How can amino acids in the polar acidic class be characterized?

A

Amino acids in the polar acidic class have ionized carboxyl groups in their side chains, resulting in a negative charge.

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54
Q

What is unique about the side chains of amino acids in the polar basic class?

A

Amino acids in the polar basic class are basic because their side chains react with water to release a hydroxide anion, resulting in a positively charged state.

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55
Q

What is the significance of amino acids in the diet?

A

All amino acids are essential for normal tissue growth and development.

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56
Q

How are “essential amino acids” defined?

A

The term “essential amino acids” is reserved for amino acids that must be supplied in the diet for proper growth and development.

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57
Q

Why must essential amino acids be obtained from the diet?

A

Essential amino acids must be supplied in the diet because there are no biochemical pathways available for their synthesis, or the available pathways do not provide adequate amounts for proper nutrition.

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58
Q

What does the acronym “PVT. TIM HALL” stand for?

A

P(Phenylalanine)
Val (Valine)
Thr (Threonine)
Trp (Tryptophan)
Ile (Isoleucine)
Met (Methionine)
His (Histidine)
Arg (Arginine)
Leu (Leucine)
Lys (Lysine)

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59
Q

Are there any exceptions to the essentiality of all amino acids in “PVT. TIM HALL”?

A

Yes, His (Histidine) and Arg (Arginine) are semi-essential because they are not synthesized in sufficient quantities during infancy, making them essential for infants.

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60
Q

What is the α-carbon attached to in an amino acid?

A

The α-carbon is attached to a carboxyl group (̶ COOH) and an amino group (̶ NH2).

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61
Q

What happens to the carboxyl group and amino group in an amino acid at physiologic pH?

A

At physiologic pH, the carboxyl group becomes –COO- (negatively charged), and the amino group becomes –NH3+ (positively charged).

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61
Q

top 10 complete vegetarian protein foods with all the essential amino acids

A
  1. firm tofu
  2. lentils
  3. low-fat yogurt
  4. cottage cheese
  5. green peas
  6. squash and pumpkin seeds
  7. quinoa
  8. peanut butter
  9. eggs
  10. mushrooms
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62
Q

What is the term for a neutral molecule with an equal number of positive and negative charges?

A

A neutral molecule with an equal number of positive and negative charges is called a zwitterion, derived from the German word “zwitter,” meaning “hybrid” or “hermaphrodite.”

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63
Q

What are the physical properties of amino acids?

A

Amino acids are white crystalline solids with high melting points and high water solubilities.

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64
Q

What causes the formation of zwitterions in amino acids?

A

The two charged groups, the basic amino group, and the carboxylic acid, at the two ends of amino acids lead to internal proton transfer, forming zwitterions.

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65
Q

How can the net charge on zwitterions be influenced?

A

The net charge on zwitterions can be affected by changing the pH of the solution in which they are found.

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66
Q

What is the term for the pH point at which there is no net charge on the zwitterions?

A

The pH point at which there is no net charge on the zwitterions is called the isoelectric point (pI).

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67
Q

What is the more accurate description of the structure of amino acids in aqueous solution at physiological pH?

A

In aqueous solution at pH 7 (physiological pH), amino acids are more accurately described as “zwitterions,” which are the product of an acid-base reaction between the carboxylic acid and the amine.

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68
Q

When do the charges on an amino acid balance out to zero?

A

The charges on an amino acid balance out to zero at one specific pH value, known as the isoelectric point (pI). At this pH, the amino acid will not migrate in an applied electric field.

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69
Q

What is the charge of a molecule below the isoelectric point?

A

Net positive charge

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70
Q

What is the charge of a molecule above the isoelectric point?

A

Net negative charge

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71
Q

How do you test the charge of an amino acid molecule at different pH values?

A

Electrophoresis

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72
Q

Explain Electrophoresis

A
  • a process that separates a mixture of amino acids by the nature of their isoelectric point. At a given fixed pH, any amino acid will have its own unique concentration of positively and negatively charged forms.
  • applying a sample of the amino acid to specially
    treated paper or gel and applying an electric field at different pH values
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73
Q

Electrophoresis: What happens to a molecule with a net charge of zero in an electric field?

A

It does not migrate in an electric field.

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74
Q

How does a molecule with a positive charge behave in an electric field?

A

It migrates towards the cathode (-).

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75
Q

How does a molecule with a negative charge behave in an electric field?

A

It migrates towards the anode (+).

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76
Q

Is the carboxylic group weakly basic or weakly acidic?

A

Weakly acidic

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77
Q

What is the net charge of a carboxylic acid?

A

+1

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78
Q

Is the ammonium group weakly acidic or weakly basic?

A

Weakly acidic

79
Q

What is the net charge of an amine formed from the ammonium group?

A

-1

80
Q

What is the carboxylic group, and what makes it weakly basic?

A

The carboxylic group is a functional group consisting of a carbon atom double-bonded to an oxygen atom and single-bonded to an oxygen atom, which is also bonded to a hydrogen atom (COOH). It is weakly basic because the oxygen atom with a lone pair can accept a proton (H+), although it is primarily known for its acidic properties.

81
Q

How does the carboxylic group become acidic, and what is the net charge of a carboxylic acid?

A

In its acidic form, the hydrogen atom attached to the oxygen in the carboxylic group can be donated as a proton (H+), forming a carboxylic acid (COOH) with a net charge of +1. This is because it loses an electron (H+) during ionization.

82
Q

What is the ammonium group, and why is it considered weakly acidic?

A

The ammonium group consists of a nitrogen atom bonded to four hydrogen atoms (NH4+). It is considered weakly acidic because the nitrogen atom can donate a proton (H+), even though it is primarily known for its basic properties.

83
Q

Describe the transformation of the ammonium group into an amine and its net charge.

A

In its basic form, the nitrogen atom in the ammonium group can accept a proton, leading to the deprotonation of one of the hydrogen atoms. This results in the formation of an amine (NH3) with a net charge of -1 because it gains an electron (H+) during the deprotonation process.

84
Q

What are amphoteric properties, and how do they apply to the carboxylic and ammonium groups?

A

Amphoteric properties mean that a substance can act as both a weak acid and a weak base, depending on the conditions and its ionization states. The carboxylic group is known for its acidic behavior when donating a proton, while the ammonium group is known for its basic behavior when accepting a proton, exemplifying amphoteric characteristics.

85
Q

At low pH, what is the dominant form of a typical amino acid with a neutral side chain?

A

The positively charged form (NH3+) dominates.

86
Q

What is the predominant form of the amino acid at its isoelectric point (pI)?

A

At the isoelectric point (pI), the zwitterionic form (NH3+ and COO-) dominates.

87
Q

At high pH, what form of the amino acid is predominantly observed?

A

The negatively charged form (COO-) dominates at high pH

88
Q

How is the pI calculated for a molecule with both acidic and basic groups?

A

The pI is calculated by averaging the pKa values of the molecule’s acidic and basic functional groups. pI = (pKa1 + pKa2) / 2

89
Q

How is the Henderson-Hasselbalch equation related to the isoelectric point (pI)?

A

The Henderson-Hasselbalch equation is related to the isoelectric point (pI) by indicating that when the pH of a solution equals the pKa of a molecule, that molecule is at its isoelectric point. At the pI, the molecule has no net charge, and it is exactly 50% dissociated into its acidic and basic forms.

90
Q

What is the structure of the acidic side chain found in amino acids, and how does it differ from a regular amino acid side chain?

A

The acidic side chain in amino acids consists of a carboxyl group (COOH) attached to the carbon atom of the amino acid’s main chain. It differs from a regular amino acid side chain because it has an additional carboxyl group, which can readily donate a proton (H+), making it an acidic functional group.

91
Q

In rare cases, at very high pH values, what can be the net charge of amino acids with acidic side chains?

A

In rare cases, at very high pH values, these amino acids can have a net charge of -2 if the carboxyl group in the side chain loses an additional proton.

92
Q

The isoelectric point (pI) of amino acids with basic side chains, such as lysine (Lys), arginine (Arg), and histidine (His), involves a process that begins with a __ dominating at very low pH.

A

doubly positively charged form (+2)

93
Q

At very low pH, what is the dominant charge of amino acids with basic side chains?

A

At very low pH, the dominant charge is +2 due to the doubly positively charged form.

94
Q

What happens to the net charge of amino acids with basic side chains as the pH increases from low values to the pI?

A

The net charge decreases from +2 to +1 as the pH increases to intermediate levels, with the carboxyl group losing a proton.

95
Q

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

A

electrophoresis

96
Q

What is the typical material used in electrophoresis for amino acid identification? What is its purpose?

A
  • paper or gel (polyacrylamide) as the medium.
  • saturated with a buffer solution, which helps maintain a stable pH environment during the separation process.
97
Q

How is a solution of unknown amino acids introduced in electrophoresis?

A

a solution of unknown amino acids is placed at the center of the paper or gel.

98
Q

What happens when electrodes are connected to the ends of the paper in electrophoresis?

A

When electrodes are connected to the ends of the paper, an electric current is allowed to pass through the solution, creating an electric field for the separation of amino acids.

99
Q

What is the purpose of spraying ninhydrin in electrophoresis?

A

ninhydrin is sprayed on the paper or gel. It reacts with amino acids to produce colored products, typically green or blue, which aid in the identification and visualization of the separated amino acids.

100
Q

What is ion exchange chromatography used for in the separation of biomolecules?

A

Ion exchange chromatography is used to separate biomolecules based on their net charge, utilizing interactions between charged functional groups on the stationary phase and oppositely charged ions of the biomolecules.

101
Q

What is the primary principle behind size exclusion chromatography (SEC)?

A

Size exclusion chromatography separates biomolecules based on their size or molecular weight, with larger molecules eluting faster as they are excluded from the porous polymer beads of the stationary phase.

102
Q

What is the fundamental concept behind affinity chromatography?

A

Affinity chromatography separates biomolecules based on their specific binding affinity for a polymer-bound ligand immobilized on the stationary phase, allowing for highly selective and precise separations.

103
Q

What are proteins composed of at the molecular level?

A

Proteins are composed of linear polymers of L-α-amino acids.

104
Q

How are amino acids linked together in protein chains?

A

The carboxyl group of one amino acid is linked to the amino group of another amino acid through an amide bond, forming a peptide linkage.

105
Q

What type of chemical reaction occurs during the formation of a peptide bond?

A

dehydration reaction in which water is released.

106
Q

What is the product of condensing or dehydrating two amino acids?

A

dipeptide

107
Q

How is the N-terminal amino acid in a protein chain identified?

A

The amino acid with a free α-NH3+ group is the amino-terminal amino acid (N-terminal for short).

108
Q

What is the C-terminal amino acid in a protein chain?

A

The amino acid with a free -COO- group is known as the carboxyl-terminal amino acid (C-terminal for short).

109
Q

How are amino acid structures typically written in diagrams?

A

N-terminal on the left side of the diagram.

110
Q

What is the difference between the terms “protein” and “peptide” in the context of amino acid chains?

A

In general, “protein” is used for molecules composed of over 50 amino acids, while “peptide” is used for molecules containing fewer than 50 amino acids.

111
Q

How is the naming of peptides determined?

A

In the naming of peptides, the far right amino acid residue retains the name of the amino acid.

112
Q

What is the general rule for changing the names of amino acids in peptides?

A

For all amino acids (except tryptophan), the suffix -ine or -ic acid is replaced by -yl in the naming of peptides.

113
Q

How is tryptophan named when it is part of a peptide?

A

Tryptophan is named tryptophanyl when it is part of a peptide.

114
Q

What is the common name for the dipeptide Asp-Phe?

A

Aspartame

115
Q

What is the physiological significance of the tripeptide Glutathione (Glu-Cys-Gly)?

A

functions as an antioxidant and regulates oxidation-reduction reactions in the body, protecting cellular contents from oxidizing agents (peroxides and superoxides)

116
Q

What are Enkephalins, and what is their role in the body?

A

Enkephalins are natural painkillers that bind to receptors in the brain, providing relief from pain. They are involved in the runner’s high, pain relief from injuries, and the effects of acupuncture.

117
Q

What are the functions of Oxytocin and Vasopressin?

A

Oxytocin stimulates uterine contractions during labor, while Vasopressin is an antidiuretic hormone that regulates blood pressure by controlling water reabsorption in the kidneys.

118
Q

What is the caloric content of aspartame, and how does its sweetness compare to sucrose?

A

Aspartame has the same caloric content as sucrose but is approximately 180 times sweeter.

119
Q

Why must both amino acids in aspartame be in the L-form for it to taste sweet?

A

Both amino acids in aspartame must be in the L-form for sweetness, while the L-D, D-L, and D-D forms taste bitter.

120
Q

In Glutathione, how is Glutamic acid (Glu) bonded to Cysteine (Cys)?

A

In Glutathione, Glu is bonded to Cys through the side-chain carboxyl group rather than through the α-carbon carboxyl group.

121
Q
  • partly responsible for triggering pain, welt formation (scratches)
  • movement of smooth muscle and lowering of blood pressure
A

Bradykinin

122
Q

completely inactive, hence, the name is bogus or false

A

Boguskinin

123
Q

a variant of hemoglobin that has specific genetic mutations or changes, which can affect the oxygen-carrying capacity of red blood cells.

A

Georgetown hemoglobin (HbG)

124
Q

What is the primary difference in amino acids in sickle cell hemoglobin (HbS)?

A

HbS differs from HbA by having a valine (Val) amino acid at position 6 in the β-globin chain instead of glutamic acid (Glu).

125
Q

What amino acid is found at position 6 in the β-globin chain of normal hemoglobin (HbA)?

A

Normal hemoglobin (HbA) has glutamic acid (Glu) at position 6 in the β-globin chain.

126
Q

What does the primary structure of a protein refer to?

A

The primary structure of a protein is the amino acid sequence of the polypeptide chain, resulting from covalent bonding between the amino acids, specifically the peptide bonds. Each protein has a unique primary structure with different amino acids in distinct positions along the chain.

127
Q

What is the significance of resonance and rigidity in peptide bonds?

A

Peptide bonds exhibit resonance and rigidity due to their partial double-bond character. This contributes to the stability and structure of proteins.

128
Q

Why is a peptide bond said to have a partial double bond character?

A

A peptide bond is considered to have a partial double bond character because of its planarity and limited rotation, which contributes to protein stability.

129
Q

How many of the three single bonds in a peptide backbone allow free rotation?

A

There is free rotation around only two of the three single bonds in a peptide backbone.

130
Q

Why are R groups on adjacent amino acids found on opposite sides of the peptide chain?

A

R groups on adjacent amino acids are positioned on opposite sides of the chain because of the rigidity of the peptide bond, which restricts rotation and enforces a fixed orientation in the protein structure.

131
Q

What defines the formation of a secondary structure in a protein?

A

Secondary structure in a protein arises when the primary sequence of the polypeptide folds into regularly repeating structures.

132
Q

What forces lead to the creation of secondary structures in proteins?

A

Secondary structure results from hydrogen bonding between the amide hydrogens (N—H) and carbonyl oxygens (C=O) of the peptide bonds.

133
Q

Are all regions of a protein’s secondary structure well-defined?

A

No, not all regions have a clearly defined secondary structure; some regions in proteins are random or nonregular in structure.

134
Q

What is the most common type of secondary structure in proteins?

A

coiled, helical structure.

135
Q

What are the important features of an α-helix in protein secondary structure?

A
  • Each amide H and carbonyl O is involved in hydrogen bonds, locking the helix in place.
  • The carbonyl O links to the amide H 4 amino acids away.
  • Hydrogen bonds in the helix are parallel to the long axis.
  • The helix is right-handed.
  • The repeat distance or pitch is 5.4 angstroms.
  • There are approximately 3.6 amino acids per turn in the helix.
136
Q

How are fibrous proteins arranged in terms of their secondary structure?

A

fibrous proteins are arranged in a secondary structure of fibers or sheets, typically featuring only one type of secondary structure.

137
Q

What is a characteristic feature of the secondary structure in fibrils formed by fibrous proteins?

A

In fibrils, you often find a repeated coiling of α-helices as a characteristic feature.

138
Q

What is the secondary structure known as the “β-pleated sheet”?

A

The β-pleated sheet is the second most common secondary structure in proteins, which appears similar to folds of fabric.

139
Q

How are all the carbonyl oxygen (O) and amide hydrogen (H) atoms involved in β-pleated sheets?

A

In β-pleated sheets, all the carbonyl oxygen (O) and amide hydrogen (H) atoms are involved in hydrogen bonds, with the polypeptide chain nearly completely extended.

140
Q

What are the two possible orientations of β-pleated sheets?

A

Parallel, if the N-termini of adjacent chains are head-to-head.
Antiparallel, if the N-terminus of one chain is aligned with the C-terminus of the other.

141
Q

What is the tertiary structure of a protein, and how does it differ from secondary structure?

A

Tertiary structure is the three-dimensional structure of a protein, distinct from secondary structure, and it is classified as the highest level of protein structure.

142
Q

What maintains the globular tertiary structure of proteins, and how is it formed?

A

Globular tertiary structure forms spontaneously and is maintained by interactions among the side chains or R groups of amino acids.

143
Q

What are the types of interactions that maintain the tertiary structure of proteins?

A
  • Disulfide bridges: Covalent bonds between two cysteine residues, the strongest of the tertiary bonds.
  • Salt bridges (ionic interactions): Attraction between ionic side chains -COO- and -NH3+.
  • Hydrogen bonds between polar residue side chains.
  • Hydrophobic interactions: Attraction between two nonpolar groups due to mutual repulsion of water.
144
Q

What is the quaternary structure of proteins, and how is it defined?

A

The quaternary structure of proteins is the functional form of many proteins, which is not that of a single polypeptide chain but an aggregate of several globular peptides. It is defined as the arrangement of subunits or peptides that form a larger protein.

145
Q

What is a subunit in the context of quaternary structure?

A

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

146
Q

How is a quaternary structure maintained?

A

Quaternary structure is maintained by the same forces that are active in maintaining tertiary structure, including interactions among side chains, hydrogen bonds, disulfide bridges, and hydrophobic interactions.

147
Q

What are some of the functions of fibrous proteins based on their shape?

A

Fibrous proteins are involved in providing mechanical strength, serving as structural components, and facilitating movement in the body.

148
Q

What are some of the functions of globular proteins based on their shape?

A

Globular proteins play roles in transport, regulation, and acting as enzymes in various biological processes.

149
Q

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

A

conjugated proteins

150
Q

What is a nucleoprotein, and what prosthetic group is associated with it? Give example.

A

Nucleoprotein is a class of conjugated proteins, and its associated prosthetic group is nucleic acids. An example of a nucleoprotein is found in viruses.

151
Q

What is a lipoprotein, and what prosthetic group is associated with it? Give example.

A

Lipoprotein is a class of conjugated proteins, and its associated prosthetic group is lipids. Serum lipoproteins are an example of lipoproteins.

152
Q

What is a glycoprotein, and what prosthetic group is associated with it? Give example.

A

Glycoprotein is a class of conjugated proteins, and its associated prosthetic group is carbohydrates. Mucin in saliva is an example of a glycoprotein.

153
Q

What is a phosphoprotein, and what prosthetic group is associated with it? Give example.

A

Phosphoprotein is a class of conjugated proteins, and its associated prosthetic group is the phosphate group. An example of a phosphoprotein is casein in milk.

154
Q

What is a hemoprotein, and what prosthetic group is associated with it? Give examples.

A

hemoprotein is a class of conjugated proteins, and its associated prosthetic group is heme. Hemoglobin and cytochromes are examples of hemoproteins.

155
Q

What is a metalloprotein, and what prosthetic groups are associated with it? Give examples.

A

Metalloprotein is a class of conjugated proteins, and it may have prosthetic groups such as iron and zinc. Examples include ferritin and hemoglobin.

156
Q

What is determined by the formation of covalent peptide bonds between amino acids?

A

primary structure of proteins

157
Q

What results from hydrogen bonding between amide hydrogens and carbonyl oxygens of peptide bonds in proteins?

A

Secondary structure in proteins, which includes α-helices and β-sheets

158
Q

What is involved in the overall folding of the entire polypeptide chain and interactions between different amino acid side chains in proteins?

A

Tertiary structure in proteins

159
Q

How does oxygen transfer from hemoglobin to myoglobin?

A

Oxygen is transferred from hemoglobin to myoglobin because myoglobin has a stronger attraction for oxygen than hemoglobin does.

160
Q

How does myoglobin’s oxygen storage capacity benefit muscle cells?

A

Myoglobin’s oxygen storage capacity provides a local oxygen reserve for muscle cells, allowing them to meet their high energy demands during physical activity.

161
Q

What is the main role of hemoglobin in the bloodstream?

A

Hemoglobin in the bloodstream carries oxygen from the lungs to various tissues and organs in the body.

162
Q

What is the common feature in the proteins hemoglobin and myoglobin?

A

The heme group is an essential component of both hemoglobin and myoglobin.

163
Q

What serves as the oxygen binding site in the heme group?

A

The Fe2+ ion (ferrous ion) in the heme group functions as the oxygen binding site.

164
Q

How many molecules of oxygen (O2) can a single heme group in hemoglobin hold?

A

Each heme group in hemoglobin can hold one molecule of oxygen (O2).

165
Q

What happens during denaturation of a protein?

A

Denaturation is the loss of the organized structure of a globular protein, which does not alter the primary structure but disrupts the secondary, tertiary, and quaternary protein structures.

166
Q

Give examples of factors that can cause protein denaturation.

A
  • extremes of temperature
  • pH
  • heat
  • organic compounds that break apart H bonds
  • acids, bases
  • heavy metal ions
  • agitation
167
Q

What is the main outcome of protein hydrolysis?

A

Protein hydrolysis breaks peptide bonds, resulting in smaller peptides and amino acids.

168
Q

When does protein hydrolysis occur in the body?

A

Protein hydrolysis occurs in the body when amino acids are needed for synthesizing new proteins and repairing tissues.

169
Q

What conditions are required for protein hydrolysis in the lab?

A

In the lab, protein hydrolysis requires acid or base, water, and heat to break peptide bonds.

170
Q

How is protein hydrolysis catalyzed in the body?

A

In the body, enzymes catalyze the hydrolysis of proteins, breaking peptide bonds and releasing amino acids for various biological processes.

171
Q

How is denaturation of egg white proteins achieved for consumption?

A

Cooking denatures egg white proteins, making them utilizable by our system. (Heat and UV)

172
Q

How does sunburn affect proteins in the body?

A

Sunburn causes denaturation of proteins in the body. (Heat and UV)

173
Q

What role do heavy metal ions like Hg2+, Pb2+, and Ag+ play in protein denaturation?

A

Heavy metal ions are used as antiseptics in low concentrations but act as poisons in higher concentrations. They can precipitate proteins in body tissues when ingested.

174
Q

How can heavy metal ion poisoning be treated?

A

Effective treatment for heavy metal ion poisoning involves feeding with egg white, followed by an emetic. The egg white forms a complex with the poison and is taken out of circulation by the emetic (a medicine or other substance that causes vomiting).

175
Q

How do organic compounds like soap, detergents, phenol, and aliphatic alcohol affect protein structure?

A

The hydrophobic portions of these compounds interact with the hydrophobic core of proteins, while the hydrophilic portion forms hydrogen bonds with the aqueous environment. This interaction causes swelling and unfolding of protein molecules.

176
Q

What are the basic steps involved in the determination of amino acid sequence in proteins?

A

The procedure involves hydrolysis (acid, alkali, or enzyme), identification of the hydrolysis products, and fitting the pieces together like a jigsaw puzzle.

177
Q

involves heating a protein in the presence of 6N HCl in a sealed tube at 110°C for a period of 10–100 hours. It completely hydrolyzes the protein but destroys Trp and partially damages Ser, Thr, and Tyr.

A

acid hydrolysis

178
Q

entails heating a protein in the presence of 4N NaOH in a sealed tube for 10–100 hours. It doesn’t damage Trp but destroys Arg, Cys, Thr, Ser, and partially deaminates some amino acids.

A

alkali hydrolysis

179
Q

cleaves peptide bonds on the carboxyl-terminal side of methionine residues. This cleavage produces relatively large and few peptides, making it useful for reducing the size of polypeptide segments for identification and sequencing.

A

cyanogen bromide

180
Q

The process of breaking down proteins into smaller peptide fragments using proteases and peptidases for sequence determination.

A

Enzymatic hydrolysis

181
Q

Enzymes that cleave external peptide bonds, with aminopeptidases working from the N-terminal end and carboxypeptidases working from the C-terminal end of the polypeptide.

A

The role of exopeptidases in enzymatic hydrolysis

182
Q

sequentially cleave peptide bonds, starting at the N-terminal end of a polypeptide, aiding in sequence determination.

A

Aminopeptidases

183
Q

sequentially cleave peptide bonds, starting at the C-terminal end of the polypeptide, helping to identify the amino acid sequence of a peptide.

A

Carboxypeptidases

184
Q

The advantages of using enzymatic hydrolysis for protein sequencing.

A

Controlled cleavage of peptide bonds, making it a valuable method for determining the sequence of amino acids in proteins and peptides.

185
Q

enzymes that cleave internal peptide bonds

A

Endopeptidases (Enzymatic Hydrolysis)

186
Q

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

A

trypsin

187
Q

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

A

Chymotrypsin

188
Q

cleaves on the carboxyl side of Gly and Ala

A

Elastase

189
Q

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

A

pepsin

190
Q

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

191
Q

The key reagent in Sanger’s method for identifying the N-terminus is __. It reacts with the__ of the N-terminal amino acid.

__ cleaves all the peptide bonds leaving a mixture of amino acids, only one of which (the N-terminus) bears a 2,4-DNP group.

A
  • 1-fluoro-2,4-dinitrobenzene
  • amino nitrogen
  • Acid hydrolysis
192
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
193
Q

The key reagent in the Edman degradation is __. It reacts with the __ of the N-terminal amino acid. In labeling, it produces __, then treated with HCl in an anhydrous solvent. The N-terminal amino acid is cleaved from the remainder of the peptide. Under the conditions of its formation, the thiazolone rearranges to a __. The PTH derivative is isolated and identified. The remainder of the peptide is subjected to a second Edman degradation

A
  • phenyl isothiocyanate
  • amino nitrogen
  • phenylthiocarbamoyl (PTC) derivative
  • phenylthiohydantoin (PTH) derivative
194
Q

reacts with all amino acids whose carboxyl group is bound in peptide linkage, creating amino acyl hydrazides. Only the C-terminal amino acid is spared.

A

hydrazine (NH2NH2) (hydrazine method)

Biomolecules CHM040 (12 decks)

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