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CHM040-Biomolecules > Chapter 3_Protein Structure and Function > Flashcards

Chapter 3_Protein Structure and Function Flashcards

1
Q

Derived from the Greek word

A

proteios meaning “first” to indicate the central
roles that proteins play in living organisms

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2
Q

are the indispensable agents of biological function

A

Protein

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3
Q

are the building blocks of proteins.

A

Amino Acid

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4
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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5
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, 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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6
Q

Functions of proteins:

A

1)Enzymes
2) Defense Proteins
3) Transport Protein
4)Regulatory Proteins
5) Structural Proteins
6)Movement Proteins
7)Nutrients

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7
Q

Functions of proteins:
Enzymes

A

are biological catalysts. Reactions that would take days or weeks or require
extremely high temperatures without enzymes are completed in an instant.

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8
Q

Functions of proteins:
(2) Defense proteins

A

include antibodies (also called immunoglobulins) which are specific protein molecules produced by specialized cells of the immune system in response to foreign antigens.

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9
Q

Functions of proteins:
(3) Transport proteins

A

carry materials from one place to
another in the body.

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10
Q

Transferrin

A

transports iron from the liver to the bone marrow, where it is used to synthesize the
heme group for hemoglobin.

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11
Q

Transferrin is synthesized and
secreted

A

into serum mostly by the liver. Synthesis of
transferrin is regulated by iron.

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12
Q

The proteins hemoglobin and
myoglobin

A

are responsible for transport and storage of oxygen in higher organisms, respectively.

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13
Q

Functions of proteins:
(4) Regulatory proteins

A

control many aspects of cell function, including metabolism and reproduction. We can function only within a limited set of conditions.

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14
Q

Functions of proteins:
(5) Structural proteins

A

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

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15
Q

Functions of proteins:
(6) Movement proteins

A

are necessary for all forms of movement

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16
Q

Functions of proteins:
(7) Nutrient proteins

A

serve as sources of amino acids for embryos or infants. Egg albumen and casein in milk are examples of nutrient storage proteins.

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17
Q

these compounds contain both an amine and an acid

A

Amino Acids

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18
Q

Amino Acids

A

Hundreds are formed both naturally and synthetically; Only 20 are common in nature; All 20 are α-amino acids; 19 out of the 20 are stereoisomers (Glycine does not have a chiral carbon)

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19
Q

is the only common amino acid that is
not chiral

A

Glycine

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20
Q
  • Nonpolar Class
A

class has hydrophobic R groups

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21
Q

Polar, neutral

A

have a high affinity for water, but are not ionic at pH

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22
Q

Polar acidic (Negatively charged) have ionized carboxyl groups in their side chains

A

(Negatively charged) have ionized carboxyl groups in their side chains

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23
Q

Polar basic

A

(Positively charged) are basic as the side chain reacts with water to release a hydroxide anion

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24
Q

The terrm __________ is reserved for those amino acids that must be supplied in the diet for proper growth and development.

A

Essential Amino Acid

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25
Q

“PVT. TIM HALL”

A

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

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26
Q

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

A

His and Arg

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27
Q

α-carbon is attached to a:

A
  • Carboxyl group (̶ COOH)
  • Amino group ( ̶ NH2)
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28
Q
  • Carboxyl group
A

(̶ COOH)

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29
Q
  • Amino group
A

( ̶ NH2)

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30
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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31
Q

At physiologic pH the amino acid has:
Carboxyl group in

A

–COO-

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32
Q

At physiologic pH the amino acid has:
Amino group in

A

–NH3+

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33
Q

Neutral molecule with equal number of + and – charges is called

A

a zwitterion

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34
Q

(from the German word “zwitter” which means “hybrid” or “hermaphrodite”)

A

zwitterion

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35
Q

Amino acids are ________ with _______ and ________.

A

white crystalline solids
high melting points
high water solubilities

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36
Q

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

A

isoelectric point (pI)

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37
Q

The isoelectric point (pI)

A

is the pH at which it bears no net charge.

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38
Q

At pH values below and above the isoelectric point, the molecule will bear a
____ or _______ , respectively

A

net positive or net negative charge

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39
Q

A molecule with a net charge of zero will not migrate in an electric field, whereas one bearing a positive (+) or negative (-) charge will migrate towards the ________ or _______, respectively.

A

cathode (-) or anode (+)

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40
Q

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

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41
Q

The amino acid carries a POSITIVE
CHARGE at pH<pI and migrates to
the

A

NEGATIVE ELECTRODE (cathode)

42
Q

The amino acid carries a NEGATIVE
CHARGE at pH>pI and migrates to
the

A

POSITIVE ELECTRODE (anode)

42
Q

Linkage is an _____ or _______.

A

amide bond or peptide linkage

43
Q

Carboxyl group of one amino acid is linked to the amino group of __________.

A

another amino acid

44
Q

Condensing or dehydrating two amino acids produces

A

a dipeptide

45
Q

Amino acid with a free a-NH3+ group is the

A

amino terminal amino acid, N-terminal for short

46
Q

Amino acid with a free –COO ̶group is the

A

carboxyl terminal amino acid, C-terminal for short

47
Q

Amino acid structures are written with the N-terminal ____ ___ _____.

A

on the left

48
Q

amino acids are polymerized into ____ and ____.

A

Proteins and peptides

49
Q

In general, protein is used for molecules composed of over 50 amino acids

A

over 50 amino acids

50
Q

_________ is used for molecules of less than 50 amino acids

A

Peptide

51
Q

Sold under the trade names Nutrasweet and Equal

A

Aspartame (Asp-Phe)

52
Q

is the artificial sweetener used in
almost every diet food on the market today.

A

Aspartame (Asp-Phe)

53
Q

It functions as an antioxidant, protecting cellular contents from oxidizing agents such as peroxides and superoxides

A

Glutathione (Glu-Cys-Gly)

54
Q

natural painkillers produced in the body; bind to receptors in the brain to give relief from pain.

A

Enkephalins

55
Q

This effect appears to be responsible for the runner’s high, for the temporary loss of pain when severe injury occurs, and for the analgesic effects of acupuncture.

A

Enkephalins and endorphins -

56
Q

stimulates uterine contractions in labor

A

Oxytocin

57
Q

is an antidiuretic hormone that regulates blood pressure by adjusting the amount of water reabsorbed by the kidneys.

A

vasopressin

58
Q

Primary structure is the ____________ of the polypeptide chain

A

amino acid sequence

59
Q

A result of covalent bonding between the amino acids

A

the peptide bonds

60
Q

R groups on adjacent amino acids are____________ because of the rigid peptide bond.

A

on opposite sides of the chain

61
Q

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

A

Secondary Structure forms

62
Q

Secondary structure results from ________between the ______ and ______ of the peptide bonds

A

hydrogen bonding; amide hydrogens (N—H) ;carbonyl oxygens (C=O)

63
Q

Most common type of secondary structure

A

Coiled and Helical

64
Q

The Secondary Structure of Proteins: α-Helix: Important features:

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
65
Q

The three-dimensional structure, which is distinct
from secondary structure

A

Tertiary Structure

66
Q

forms spontaneously and is maintained by
interactions among the side chains or R groups

A

Globular tertiary structure

67
Q

defines the biological function of proteins

A

Tertiary Structures

68
Q

Types of Interactions Maintaining Tertiary Structure

A

Disulfide bridges
Salt bridges
Hydrogen bonds
Hydrophobic interactions

69
Q

bridges between two cysteine residues

A

Disulfide bridges

70
Q

between ionic side chains –COO– and –NH3+

A

Salt Bridges

71
Q

between polar residue side chains

A

Hydrogen Bond

72
Q

two nonpolar groups are attracted by a mutual
repulsion of water

A

Hydrophobic interactions

73
Q

The functional form of many proteins is not that of a single polypeptide chain but an aggregate of several globular peptides

A

The Quaternary Structure of Proteins

74
Q

the arrangement of subunits or peptides that form a
larger protein

A

Quaternary structure

75
Q

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

A

Subunit

76
Q

Quaternary structure is

A

maintained by the same forces which are active in maintaining tertiary structure

77
Q

Protein Functions Follow Shape:
Fibrous proteins:

A
  • Mechanical strength
  • Structural components
  • Movement
78
Q

Protein Functions Follow Shape:
Globular proteins:

A
  • Transport
  • Regulatory
  • Enzymes
79
Q

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

A

Conjugated Proteins

80
Q

is the oxygentransport protein of higher animals

A

Hemoglobin

81
Q

is the oxygen storage protein of skeletal muscle

A

Myoglobin

82
Q

Oxygen is transferred from hemoglobin to myoglobin as

A

myoglobin has a stronger attraction for oxygen than
hemoglobin does

83
Q

is an essential component of the proteins
hemoglobin and myoglobin

A

Heme Group

84
Q

ion in the heme group is the oxygen binding site

A
  • Fe2+
85
Q

is the loss of organized structure of a globular protein

A

Denaturation

86
Q

Denaturation

A

Does not alter primary structure; the disruption of bonds in the secondary, tertiary, and quaternary protein structures

87
Q

Trypsin Cleaves at

A

Carboxyl end
Lysine and Arginine

88
Q

Chymotrypsin cleaves at

A

Carboxyl Ends of
Phenylalananine; Tyrosine; tryptophan; and Leucine

89
Q

Elastase Cleaves at

A

Glycine and Alanine

90
Q

Pepsin cleaves at

A

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

91
Q

Thermolysin cleaves at

A

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

92
Q

The key reagent in Sanger’s method for identifying the N-terminus

A

1-fluoro-2,4-dinitrobenzene

93
Q

1-Fluoro-2,4-dinitrobenzene reacts with the _______

A

amino nitrogen of the N-terminal amino acid.

94
Q

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

Acid Hydrolysis

95
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

96
Q

The key reagent in the Edman degradation is

A

phenyl isothiocyanate.

96
Q

Phenyl isothiocyanate reacts with the

A

amino nitrogen of the N-terminal amino acid.

97
Q

hydrazine reacts with all amino acids whose carboxyl
group is bound in peptide linkage, creating amino acyl hydrazides.

A

Hydrazine Method

98
Q

hydrazine reacts with__________, creating ______.

A

all amino acids whose carboxyl group is bound in peptide linkage;amino acyl hydrazides.

99
Q
A

CHM040-Biomolecules (4 decks)

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