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Biochemistry > Module 03: Proteins (Stoker) > Flashcards

Module 03: Proteins (Stoker) Flashcards

1
Q

This is a naturally-occurring, unbranched polymer in which the monomer units are amino acids. Moreover, these are most abundant molecules in the cells after water – account for about 15% of a cell’s overall mass

A

Proteins

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2
Q

What elements are primarily present in proteins?

A

Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), most also contain Sulfur (S)

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3
Q

How many is the average nitrogen content of proteins by mass?

A

15.4%

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4
Q

This is an organic compound that contains both an amino (-NH2) and carboxyl (-COOH) groups attached to same carbon atom

A

Amino Acid

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5
Q

This is the compound where the amino group (NH2) and the carboxyl group is bonded)

A

Alpha Carbon

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6
Q

Based on common “R” groups, there are how many standard amino acids?

A

20 amino acids

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7
Q

Standard amino acids are divided into four groups based on the properties of R-groups, which are namely:

A

(1) Non-polar amino acids
(2) Polar amino acids
(3) Polar-neutral
(4) Polar-basic and Polar-acidic

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8
Q

These are amino acids constituted with R-groups that are non-polar or amino acids are hydrophobic-water fearing (insoluble in water)

A

Non-polar amino acids

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9
Q

Where are Non-polar amino acids located?

A

When present in proteins, they are located in the interior of protein where there is no polarity

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10
Q

How many non polar amino acids are there?

A

8 to 20 standard amino acids

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11
Q

This amino acid contains R-groups that are polar.

A

Polar Amino Acids

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12
Q

This amino acid contains polar but neutral side chains

A

Polar-neutral amino acids

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13
Q

This amino acid contain carboxyl group as part of the side chains

A

Polar acidic amino acids

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14
Q

This amino acid contain amino group as part of the side chain

A

Polar basic amino acids

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15
Q

What are the different non-polar amino acids?

A

(1) Glycine
(2) Alanine
(3) Proline
(4) Valine
(5) Isoleucine
(6) Leucine
(7) Methionine
(8) Phenylalanine
(9) Tryptophan

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16
Q

What are the different Polar Neutral Amino Acids?

A

(1) Serine
(2) Threonine
(3) Asparagine
(4) Cysteine
(5) Glutamine
(6) Tyrosine

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17
Q

What are the different Polar Basic Amino Acids?

A

(1) Lysine
(2) Arginine
(3) Histidine

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18
Q

What are the different Polar Acidic Amino Acids?

A

Glutamic and Aspartic Acids

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19
Q

Four different groups are attached to the a-carbon atom in all of the standard amino acids except ____________________.

A

Glycine

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20
Q

How many standard amino acids contain a chiral center?

A

19 to 20

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21
Q

These exhibit enantiomerism (left- and right-handed forms)

A

Chiral Centers

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22
Q

Where are L-isomers present?

A

Proteins

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23
Q

Where are D-isomers present?

A

bacteria

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23
Q

What is the rules for drawing Fischer projection formulas for amino acid structures

A

The — COOH group is put at the top, the R group at the bottom to position the carbon chain vertically

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24
Q

This is an ion with + (positive) and – (Negative) charges on the same molecule with a net zero charge

A

Zwitterion

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25
Q

In Zwitterions, what do carboxyl groups do?

A

Carboxyl groups give-up a proton to get negative charge

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26
Q

In Zwitterions, what do amino groups do?

A

Amino groups accept a proton to become positive

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27
Q

What is the state of amino acids and carboxyl groups at low pH?

A

At low pH, amino groups and carboxyl groups are protonated (gained H+)–> NH3+ and –COOH

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28
Q

What is the state of amino acids and carboxyl groups at pH 7?

A

carboxyl group –COOH is ionized to –COO-

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29
Q

What is the state of amino acids and carboxyl groups at high pH?

A

At high pH, the protonated amino –NH3+ is deprotonated –> -NH2

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30
Q

This is the pH at which the concentration of Zwitterion is maximum –> net charge is zero

A

Isoelectric point (At isoelectric point - amino acids are not attracted towards an applied electric field because they net zero charge.)

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31
Q

This is the only amino acid that has the standard amino acid with a sulfhydryl group ( — SH group).

A

Cysteine

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32
Q

What happens to cysteine in the presence of mild oxidizing agents?

A

Cysteine in the presence of mild oxidizing agents dimerizes to form a cystine molecule.

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33
Q

What comprises a cystine?

A

two cysteine residues linked via a covalent disulfide bond.

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34
Q

This pertains to a chain of covalently-linked AAs.

A

peptide.

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35
Q

The covalent bonds between amino acids in a peptide are called ____________

A

peptide bonds.

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36
Q

What are the properties of a peptide bond?

A

(1) It is formed between –COOH of one amino acid and the –NH2 of the next amino acid
(2) It is a strong bond with partial double bond character due to resonance. It resists rotation, thereby stabilizing protein structures.
(3) Can not be broken by denaturing agents but by prolonged exposure to acids or bases at elevated temperatures
(4) Usually in transconfiguration
(5) C=O and N-H can participate in H-bonding

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37
Q

This is a bond between two amino acids

A

Dipeptide

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38
Q

This is a bond between ~ 10 - 20 amino acids

A

Oligopeptide

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39
Q

This is a bond between large number of amino acids

A

Polypeptide

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39
Q

What are some examples of small peptides that are biochemically active?

A

(1) Hormones
(2) Neurotransmitters
(3) Antioxidants

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40
Q

These are examples of small peptide hormones

A

oxytocin and vasopressin

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41
Q

Where are small peptide hormones formed?

A

the pituitary gland

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42
Q

What constitutes a nonapeptide

A

(nine amino acid residues) with six of the residues held in the form of a loop by a disulfide bond formed between two cysteine residues

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43
Q

The is called the ‘love hormone’ because of its role in various behaviors, including orgasm, social recognition, bonding, and maternal behavior. It is released in response toactivation of sensory nerves during labor, breastfeeding and sexual activity.

A

Oxytocin

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43
Q

These are pentapeptide neurotransmitters produced by the brain and bind receptor within the brain help to reduce pain.

A

Enkephalins

44
Q

Where to Enkephalins bind to?

A

Opiate receptors

45
Q

What are the types of enkephalins?

A

Met-enkephalin: Tyr–Gly–Gly–Phe–Met
Leu-enkephalin: Tyr–Gly–Gly–Phe–Leu

46
Q

This is a tripeptide – is present is in high levels in most cells

A

Glutathione

47
Q

What amino acids constitute a Glutathione?

A

Glycine, Glutamine, Cysteine (where Glu is bonded to Cys through the side-chain carboxyl group.)

48
Q

What is the role of Glutathione?

A

(1) Regulates oxidation-reduction reactions
(2) Is an antioxidant and protects cellular contents from oxidizing agents such as peroxides and super oxides

49
Q

This is a dipeptide or an artificial non-saccharide sweetener 200 times sweeter than sucrose and is commonly used as a sugar substitute in foods and beverages.

A

Aspartame

50
Q

What amino acids constitute aspartame?

A

Asparagine and Phenylalanine

51
Q

This is a peptide in which at least 40 amino acid residues are present

A

Protein

52
Q

Common proteins contain_______________amino acid residues

A

400–500

53
Q

Small proteins contain _________amino acid residues

A

40–100

54
Q

This protein contains one peptide chain

A

Monomeric

55
Q

This contains more than one peptide chain

A

Multimeric

56
Q

This is a protein in which only amino acid residues are present:
More than one protein subunit may be present but all subunits contain only amino acids

A

Simple proteins

57
Q

This is a protein that has one or more non-amino acid entities (prosthetic groups) present in its structure. In this, one or more polypeptide chains may be present

A

Conjugated protein

58
Q

These type of proteins contain lipid prosthetic groups

A

Lipoproteins

59
Q

These type of proteins contain carbohydrate groups,

A

Glycoproteins

60
Q

These type of proteins contain a specific metal as prosthetic group

A

Metalloproteins

61
Q

what are the four types of structure

A

Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure

62
Q

This protein structure refers to the order in which amino acids are linked together in a protein

A

Primary Structure

63
Q

He sequenced and determined the primary structure for the first protein - Insulin

A

Frederick Sanger (1953)

64
Q

This protein structure refers to the regular arrangement of amino acids closed to one another in the linear sequence.

A

Secondary Structure

65
Q

The Secondary Structure is stabilized by what?

A

Stabilized by H-bonding between peptide bond component: carbonyl oxygen and amide H.

66
Q

This structure has a spiral structure, consisting of tightly packed, coiled polypeptide, pp backbone core:

A

Alpha-helix (-helix)

67
Q

All the peptide bonds in an alpha helix is linked to each other through?

A

Interchain Hydrogen Bonds

68
Q

What are the amino acids that disrupt an alpha helix?

A

(1) Proline because it is not geometrically compatible with the right handed spiral of the alpha helix
(2) Glutamate, Aspartic, Lysine, Arginine and Histidine because they electrostatically repel one another
(3) Tryptophan, Valine, and Isoleucine because they are bulky and present in large numbers

69
Q

These structure are completely extended amino acid chains, the surfaces appear pleated, composed of 2 or more pp chains or 2 segments of a pp, H-bonding is perpendicular to the polypeptide backbone
Side chains below or above the axis

A

Beta-Pleated Sheets

70
Q

This structure reverses the direction of a polypeptide chain, helping it form compact and globular shape

A

Beta-turns or Bends

71
Q

This protein structure pertains to the overall three-dimensional shape of a protein and results from the interactions between amino acid side chains (R groups) that are widely separated from each other.

A

Tertiary Structure

72
Q

This type of interaction pertains to the covalent, strong, between two cysteine groups, contributes to stability of 3-dimensional structure of protein

A

Disulfide bond

73
Q

This type of interaction pertains salt Bridge between charged side chains of acidic and basic amino acids
-OH, -NH2, -COOH, -CONH2

A

Electrostatic interactions

74
Q

This type of interaction pertains between polar, acidic and/or basic R groups, enhances increase in the solubility of protein with polar solvents. For H-bonding to occur, the H must be attached on O, N or F

A

H-Bonding

75
Q

This type of interaction Between non-polar side chains of amino acids, found in the interior of globular proteins interacting with other nonpolar amino acids.

A

Hydrophobic interactions

76
Q

This structure of protein refers to the organization among the various peptide chains in a multimeric protein. Moreover, this is highest level of protein organization and is only present only in proteins that have 2 or more polypeptide chains (subunits)

A

Quaternary structure

77
Q

Proteins with quartenary structure are often referred to as ________________

A

oligomeric proteins

78
Q

These protein molecules with elongated shape and are generally insoluble in water. They tend to have simple, regular, linear structures and aggregate together to form macromolecular structures, e.g., hair, nails, etc.

A

Fibrous proteins

79
Q

What kind of structures do fibrous proteins have?

A

Secondary Structures

80
Q

These protein molecules with peptide chains folded into spherical or globular shapes. They are generally hydrophobic amino acid residues in the protein core. Moreover, they function as enzymes and intracellular signaling molecules

A

Globular proteins

81
Q

These proteins are associated with cell membranes and are insoluble in water – hydrophobic amino acid residues on the surface. They help in transport of molecules across the membrane

A

Membrane proteins

82
Q

What is the structure of alpha keratin?

A

Helical in structure and 4o structure is association of alpha helices into coiled coil

83
Q

What is the structure of beta keratin?

A

4o is stacked  -pleated sheets

84
Q

What is the entailed for collagen in terms of maintaining its structure?

A

Proline (20%)

85
Q

These are best known for their catalytic role.

A

Catalytic Proteins (Enzymes)

86
Q

These are central to functioning of the body’s immune system.

A

Defense proteins: Immunoglobulins or antibodies

87
Q

These bind small biomolecules, e.g., oxygen and other ligands, and transport them to other locations in the body and release them on demand.

A

Transport proteins

88
Q

These transmit signals to coordinate biochemical processes between different cells, tissues, and organs.

A

Messenger proteins

89
Q

These amino acid regulate carbohydrate metabolism

A

Insulin and glucagon

90
Q

These are necessary for all forms of movement.

A

Contractile proteins

91
Q

These are contractile proteins that constitute a muscle.

A

actin and myosin

92
Q

They confer stiffness and rigidity

A

Structural proteins

93
Q

These span a cell membrane and help control the movement of small molecules and ions. Moreover, they have channels that help molecules can enter and exist the cell. In this, transport is very selective - allow passage of one type of molecule or ion.

A

Transmembrane proteins

94
Q

These bind (and store) small molecules.

A

Storage proteins

95
Q

This is an iron-storage protein - saves iron for use in the biosynthesis of new hemoglobin molecules

A

Ferritin

96
Q

This is an oxygen-storage protein present in muscle

A

Myoglobin

97
Q

These are often found “embedded” in the exterior surface of cell membranes - act as sites for receptor molecules. Moreover, often the molecules that bind to enzymes (catalytic proteins), thereby turning them “on” and “off,” and thus controlling enzymatic action.

A

Regulatory proteins

98
Q

These proteins are particularly important in the early stages of life - from embryo to infant.

A

Nutrient proteins

99
Q

This is the amino acid abundant in milk.

A

Casein

100
Q

This is the amino acid abundant in eggs.

A

ovalalbumin

101
Q

This is known as the reverse of peptide bond formation: This results in the generation of an amine and a carboxylic acid functional groups.

A

Hydrolysis

102
Q

This form of hydrolysis pertains to the digestion of ingested protein.

A

enzyme-catalyzed hydrolysis

103
Q

Collagen is rich in?

A

Rich in 4-hydroxyproline (5%) and 5-hydroxylysine (1%) — derivatives

104
Q

Immunoglobulin bonding to an antigen via variable region of an immunoglobulin occurs through what interactions?

A

through hydrophobic interactions, dipole – dipole interactions, and hydrogen bonds.

105
Q

This is a conjugated protein that contains lipids in addition to amino acids

A

Lipoproteins

106
Q

What is the primary role of lipoproteins?

A

They help suspend lipids and transport them through the bloodstream

107
Q

These lipoproteins transport dietary triacyclglycerols from intestine to liver and to adipose tissue.

A

Chylomicrons

108
Q

These lipoproteins transport triacyclglycerols synthesized in the liver to adipose tissue.

A

Very-low-density lipoproteins (VLDL):

109
Q

These lipoproteins transport cholesterol synthesized in the liver to cells throughout the body.

A

Low-density lipoproteins (LDL):

110
Q

These lipoproteins collect excess cholesterol from body tissues and transport it back to the liver for degradation to bile acids.

A

High-density lipoproteins (HDL)

Biochemistry (16 decks)

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