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BIOCHEM > Structure of Proteins > Flashcards

Structure of Proteins Flashcards

1
Q

The 20 amino acids commonly found in proteins are joined together by

A

peptide bonds

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2
Q

contains the information necessary to generate a protein molecule with a unique three-dimensional shape.

A

The linear sequence of the linked amino acids

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3
Q

The complexity of protein structure is best analyzed by considering the molecule in terms of four organizational levels:

A

primary, secondary, tertiary, and quaternary

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4
Q

What explains that proteins have general “rules” regarding the ways in which proteins achieve their native, functional form.

A

An examination of these hierarchies of increasing complexity has revealed that certain structural elements are repeated in a wide variety of proteins.

These repeated structural elements range from simple combinations of α-helices and β-sheets forming small motifs, to the complex folding of polypeptide domains of multifunctional proteins

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5
Q

What consists the the primary structure of the protein?

A

sequence of amino acids

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6
Q

Peptide bonds are linked on what parts of the amino acids?

A

α-carboxyl group of one amino acid and the α-amino group of another

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7
Q

Peptide bonds are resistant to what conditions?

A

conditions that denature proteins such as heating and high concentration of urea

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8
Q

Prolonged exposure of a petide bond to a strong acid or base at elevated temperatures is required to

A

break these bonds nonenzymically

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9
Q

How are amino acid sequences read?

A

read from the N- to the C-terminal

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10
Q

Linkage of many amino acids through peptide bonds results in an unbranched chain called a

A

polypeptide

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11
Q

Each component amino acid in a polypeptide is called a

A

“residue”

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12
Q

Explain how polypeptides are named

A

When a polypeptide is named, all amino acid residues have their suffixes (-ine, -an, -ic, or -ate) changed to -yl, with the exception of the C-terminal amino acid. For example, a tripeptide composed of an N-terminal valine, a glycine, and a C-terminal leucine is called valylglycylleucine.

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13
Q

Characteristics of the peptide bond

A

The peptide bond has a partial double-bond character, that is, it is shorter than a single bond and is rigid and planar

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14
Q

What allows poplypeptide bonds to assume a variety of possible configurations

A

the bonds between the α-carbons and the α-amino or α-carboxyl groups can be freely rotated

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15
Q

Polypeptide bond is almost always found in what orientation?

A

Trans, isntead of cis

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16
Q

Explain the polarity of the peptide bond

A

Like all amide linkages, the – C =O and – NH groups of the peptide bond are uncharged and neither accept nor release protons over the pH range of 2–12. Thus, the charged groups present in polypeptides consist solely of the N-terminal (α-amino) group, the C-terminal (α-carboxyl) group, and any ionized groups present in the side chains of the constituent amino acids. The – C=O and – NH groups of the peptide bond are polar, however, and are involved in hydrogen bonds (for example, in α-helices and β-sheets)

key:
– C =O and – NH uncharged
N-terminal and C-terminal are charged

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17
Q

The first step in determining the primary structure of a polypeptide is

A

to identify and quantitate its constituent amino acids

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18
Q

A purified sample of the polypeptide to be analyzed is first

A

hydrolyzed by strong acid at 110°C for 24 hours

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19
Q

what does hydrolysis by strong acid at 110c for 24 hours do to the amino acid?

A

This treatment cleaves the peptide bonds and releases the individual amino acids

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20
Q

The free amino acids after hydrolysis can be seperated by?

A

cation-exchange chromatography

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21
Q

explain cation-exchange chromatography

A

In this technique, a mixture of amino acids is applied to a column that contains a resin to which a negatively charged group is tightly attached.

[Note: If the attached group is positively charged, the column becomes an anion-exchange column.]

The amino acids bind to the column with different affinities, depending on their charges, hydrophobicity, and other characteristics.

Each amino acid is sequentially released from the chromatography column by eluting with solutions of increasing ionic strength and pH.

The separated amino acids contained in the eluate from the column are quantitated by heating them with ninhydrin (a reagent that forms a purple compound with most amino acids, ammonia, and amines).

The amount of each amino acid is determined spectrophotometrically by measuring the amount of light absorbed by the ninhydrin derivative.

The analysis described above is performed using an amino acid analyzer, an automated machine whose components

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22
Q

is a stepwise process of identifying the specific amino acid at each position in the peptide chain, beginning at the N-terminal end

A

Sequencing

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23
Q

is used to label the amino-terminal residue under mildly alkaline conditions

A

Phenylisothiocyanate, known as Edman reagent

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24
Q

Explain how Phenylisothiocyanate is used to identify the sequence of amino acids in a polypeptide chain

A

Phenylisothiocyanate, known as Edman reagent, is used to label the amino-terminal residue under mildly alkaline conditions.

The resulting phenylthiohydantoin (PTH) derivative introduces an instability in the N-terminal peptide bond such that it can be hydrolyzed without cleaving the other peptide bonds.

The identity of the amino acid derivative can then be determined.

Edman reagent can be applied repeatedly to the shortened peptide obtained in each previous cycle. The process is now automated.

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25
Q

Explain how polypeptides with more than 100 amino acids are sequenced

A

Such molecules cannot be sequenced directly from end to end.

However, these large molecules can be cleaved at specific sites and the resulting fragments sequenced.

By using more than one cleaving agent (enzymes and/or chemicals) on separate samples of the purified polypeptide, overlapping fragments can be generated that permit the proper ordering of the sequenced fragments, thereby providing a complete amino acid sequence of the large polypeptide

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26
Q

Enzymes that hydrolyze peptide bonds are termed

A

peptidases (proteases).

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27
Q

cut at the ends of proteins

A

Exopeptidases

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28
Q

Exopeptidases are divided into

A

aminopeptidases and carboxypeptidases

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29
Q

are used in determining the C-terminal amino acid

A

Carboxypeptidases

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30
Q

cleave within a protein

A

Endopeptidases

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31
Q

What are the disadvantages of determining the protein’s primary structure through DNA sequencing?

A

not being able to predict the positions of disulfide bonds in the folded chain and of not identifying any amino acids that are modified after their incorporation into the polypeptide

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32
Q

is the most common secondary protein structure

A

α-helix

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33
Q

explain the structure of a-helix

A

It is a spiral structure, consisting of a tightly packed, coiled polypeptide backbone core, with the side chains of the component amino acids extending outward from the central axis to avoid interfering sterically with each other

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34
Q

An α-helix is stabilized by

A

extensive hydrogen bonding between the peptide-bond carbonyl oxygens and amide hydrogens

35
Q

Each turn of an α-helix contains

A

3.6 amino acids

36
Q

Give examples of amino acids that disrupt an a-helix

A

Proline - not geometrically compatible

glutamate, aspartate, histidine, lysine, and arginine - forming ionic bonds or by electrostatically repelling each other

tryptophan, valine, or isoleucine - bulky side chain

37
Q

another form of secondary structure in which all of the peptide bond components are involved in hydrogen bonding.

They appear pleated

A

β-sheet

38
Q

compare b-sheet and a-helix

A

Unlike the α-helix, β-sheets are composed of two or more peptide chains (β-strands), or segments of polypeptide chains, which are almost fully extended. Note also that the hydrogen bonds are perpendicular to the polypeptide backbone in β-sheets

39
Q

β-sheet can be formed from two or more separate polypeptide chains or segments of polypeptide chains that are arranged either:

A

antiparallel to each other (with the N-terminal and C-terminal ends of the β-strands alternating)

or parallel to each other (with all the N-termini of the β-strands together)

40
Q

When the hydrogen bonds are formed between the polypeptide backbones of separate polypeptide chains, they are termed

A

interchain bonds

41
Q

What happens when a b-sheet is only made by one polypeptide chain?

A

The chain folds back on itself In this case, the hydrogen bonds are intrachain bonds.

42
Q

In globular proteins, β-sheets always have a

A

right-handed curl, or twist, when viewed along the polypeptide backbone. [Note: Twisted β-sheets often form the core of globular proteins.]

43
Q

The α-helix and β-sheet structures provide

A

maximal hydrogen bonding for peptide bond components within the interior of polypeptides.

44
Q

This secondary structure reverse the direction of a polypeptide chain, helping it form a compact, globular shape.

A

β-Bends

45
Q

β-Bends are usually found on?

A

surface of protein molecules and often include charged residues

46
Q

β-Bends are generally composed of

A

four amino acids, one of which may be proline

47
Q

the amino acid with the smallest R group, is also frequently found in β-bends.

A

Glycine,

48
Q

β-Bends are stabilized by the

A

formation of hydrogen and ionic bonds

49
Q

Approximately one half of an average globular protein is organized into repetitive structures, such as the α-helix and β-sheet. The remainder of the polypeptide chain is described as

A

having a loop or coil conformation

(have less regualr structure)

50
Q

are usually produced by the close packing of side chains from adjacent secondary structural elements.

A

Supersecondary structures

51
Q

“Tertiary” refers both to the

A

folding of domains (the basic units of structure and function, see discussion below), and to the final arrangement of domains in the polypeptide.

52
Q

are the fundamental functional and three-dimensional structural units of polypeptides.

A

Domains

53
Q

Polypeptide chains that are greater than 200 amino acids in length generally consist of how many domains

A

2 or more

54
Q

The core of a domain is built from

A

combinations of supersecondary structural elements (motifs)

55
Q

Folding of the peptide chain within a domain usually occurs dependently of folding in other domains

t/f?

A

F:
Folding of the peptide chain within a domain usually occurs independently of folding in other domains

56
Q

each domain is structurally dependent on each other from other domains in the same polypeptide chain.

t/f?

A

F: Therefore, each domain has the characteristics of a small, compact globular protein that is structurally independent of the other domains in the polypeptide chain.

57
Q

The unique three-dimensional structure of each polypeptide is determined by

A

its amino acid sequence

58
Q

guides the folding of the polypeptide to form a compact structure.

A

Interactions between the amino acid side chains

59
Q

a covalent linkage formed from the sulfhydryl group (–SH) of each of two cysteine residues to produce a cystine residue

A

Disulfide bonds

60
Q

What are the interactions stabilizing tertiary structure?

A

Disulfide bonds
Hydrophobic interactions
Hydrogen bonds
Ionic interactions

61
Q

Which amino acids rely on hydrophobic interactions in order to gain their tertiary structure?

A

Amino acids with nonpolar side chains

62
Q

Which amino acids rely on hydrogen bonds in order to gain their tertiary structure?

A

Amino acid side chains containing oxygen- or nitrogen-bound hydrogen, such as in the alcohol groups of serine and threonine

63
Q

Which amino acids rely on ionic interactions in order to gain their tertiary structure?

A

Negatively charged groups, such as the carboxylate group (–COO–) in the side chain of aspartate or glutamate

64
Q

what determines how a long polypeptide chain folds into the intricate three-dimensional shape of the functional protein.

A

Interactions between the side chains of amino acids

65
Q

Protein folding occurs where?

A

In the cell (within seconds to minutes)

66
Q

Some biologically active proteins or segments thereof lack a stable tertiary structure. They are referred to as

A

“intrinsically disordered” proteins.

67
Q

results in the unfolding and disorganization of a protein’s secondary and tertiary structures without the hydrolysis of peptide bonds

A

Protein denaturation

68
Q

Denaturing agents

A

include heat, organic solvents, strong acids or bases, detergents, and ions of heavy metals such as lead

69
Q

Denatured proteins are often

A

insoluble and precipitate from solution.

70
Q

The information needed for correct protein folding is contained in the

A

primary structure of the polypeptide

71
Q

for many proteins, folding is a facilitated process that requires a specialized group of proteins, referred to as

A

molecular chaperones and adenosine triphosphate hydrolysis

72
Q

The chaperones, also known as

A

“heat shock proteins” (Hsp)

73
Q

explain how chaperones work

A

The chaperones, also known as “heat shock proteins” (Hsp), interact with a polypeptide at various stages during the folding process. Some chaperones bind hydrophobic regions of an extended polypeptide and are important in keeping the protein unfolded until its synthesis is completed (for example, Hsp70).

Others form cage-like macromolecular structures composed of two stacked rings. The partially folded protein enters the cage, binds the central cavity through hydrophobic interactions, folds, and is released (for example, mitochondrial Hsp60).

[Note: Cage-like chaperones are sometimes referred to as “chaperonins.”]

Chaperones, then, facilitate correct protein folding by binding to and stabilizing exposed, aggregation-prone hydrophobic regions in nascent (and denatured) polypeptides, preventing premature folding.

74
Q

What are quarternary structure of proteins?

A

The arrangement of polypeptide subunits

75
Q

Subunits are held together primarily by

A

noncovalent interactions

76
Q

are proteins that perform the same function but have different primary structures.

A

Isoforms

77
Q

If the proteins function as enzymes, they are referred to as

A

isozymes

78
Q

Give examples of diseases that are caused by protein misfolding

A

Amyloid diseases and Prion diseases

79
Q

Explain amyloid diseases

A

The formation of amyloids from misfolding of protein spontaneously or due to a genetic mutation, or after an abnormal proteolytic cleavage, has been implicated in degenerative diseases such as parkinson and huntington and alzheimers

80
Q

Explain Alzheimers

A

The dominant component of the amyloid plaque that accumulates in Alzheimer disease is amyloid β (Aβ), an extracellular peptide containing 40–42 amino acid residues.

X-ray crystallography and infrared spectroscopy demonstrate a characteristic β-pleated sheet conformation in nonbranching fibrils.

This peptide, when aggregated in a β-pleated sheet configuration, is neurotoxic and is the central pathogenic event leading to the cognitive impairment characteristic of the disease.

The Aβ that is deposited in the brain in Alzheimer disease is derived by enzymic cleavages (by secretases) from the larger amyloid precursor protein, a single transmembrane protein expressed on the cell surface in the brain and other tissues.

The Aβ peptides aggregate, generating the amyloid that is found in the brain parenchyma and around blood vessels. Most cases of Alzheimer disease are not genetically based, although at least 5% of cases are familial.

A second biologic factor involved in the development of Alzheimer disease is the accumulation of neurofibrillary tangles inside neurons. A key component of these tangled fibers is an abnormal form (hyperphosphorylated and insoluble) of the tau (τ) protein, which, in its healthy version, helps in the assembly of the microtubular structure.

The defective τ appears to block the actions of its normal counterpart.

Mutations to presenilin, the catalytic subunit of γ-secretase, are the most common cause of familial AD

81
Q

Explain Prion diseases

A

A noninfectious form of PrPC (Prp= prion C = cellular), encoded by the same gene as the infectious agent, is present in normal mammalian brains on the surface of neurons and glial cells.

Thus, PrPC is a host protein. No primary structure differences or alternate posttranslational modifications have been found between the normal and the infectious forms of the protein.

The key to becoming infectious apparently lies in changes in the three-dimensional conformation of PrPC.

It has been observed that a number of α-helices present in noninfectious PrPC are replaced by β-sheets in the infectious form

82
Q

Examples of prion diseases

A

The prion protein (PrP) has been strongly implicated as the causative agent of transmissible spongiform encephalopathies (TSEs), including Creutzfeldt-Jakob disease in humans, scrapie in sheep, and bovine spongiform encephalopathy in cattle (popularly called “mad cow” disease)

83
Q

is whatyou call the functional, fully folded protein structure

A

native conformation

BIOCHEM (4 decks)

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