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BIOCHEM*2580 > FII - Lecture Slides 1 - 45 > Flashcards

FII - Lecture Slides 1 - 45 Flashcards

1
Q
A
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2
Q

What does the ribbon trace?

A

The polypeptide backbone Peptide bonds only, no side chains)

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3
Q

What is a primary structure of a protein?

A

The linear sequence of amino acids

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4
Q

What is the secondary structure of a protein?

A

The repetitive patterns, such as the alpha helices, beta pleated sheets and the “loops and turns”

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5
Q

What is the tertiary structure of a protein?

A

The overall 3D pattern of its polypeptide arrangement.

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6
Q

What is the quaternary protein structure?

A

The assembly of multiple subunits (multiple amino acid chains coming together)

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7
Q

What does it mean when a peptide bond is hydrolyzed?

A

Adding in water to break the peptide bond, in order to release the individual amino acids

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8
Q

What are enzymes?

A

Enzymes are protein that have catalytic functions

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9
Q

What type of enzymes hydrolyze peptide bonds?

A

Proteases

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10
Q

How can the amino acids be analyzed after hydrolysis of the peptide?

A

Through chromatography methods (tell you how much amino acid is present)

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11
Q

What is chemical reactivity caused by?

A

An unequal sharing of valence electrons which causes unbalanced and reaction molecules

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12
Q

What is a nucleophile?

A

A atom that has a lone pair of electrons available to share; they seek out electron deficient atoms to give them their electrons

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13
Q

What are examples of nucleophiles?

A

EN element such as Oxygen (not oxyanion), nitrogen, sulfur

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14
Q

What is the hydrolysis of peptide bonds considered to be?

A

A nucleophilic displacement (substitution)

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15
Q

In a peptide bond, what does the carbon act as?

A

An electrophile as it is electron deficient due to the double bonded oxygen taking its bonding electrons away.

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16
Q

What happens when water attacks the carbon to hydrolyze it?

A

The double bond breaks and the electrons move to the oxygen and it becomes an oxyanion.
This is temporary and unstable, so the electrons move back to the carbon where they move to the nitrogen.
The nitrogen breaks off and gains a hydrogen in the process.

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17
Q

What is the leaving group in the hydrolysis of a peptide with neutral water?

A

The amino group which allows the peptide to break.

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18
Q

What was Sanger’s Method?

A

He was able to figure out the first amino acid (N-terminus) of a protein by tagging it with fluorodinitrobenzene.

Hydrolysis released the N-terminus of the amino acid, with the yellow tag attached and you were able to identify its by chromatography.

Issue: The rest of the peptide was destroyed during hydrolysis.

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19
Q

What is the Edman Degradation method?

A

It involves two steps:
1. Coupling under basic conditions where he labels the N-terminus Amino Acid with PITC
2. Cyclization occurs under acidic conditions where he cleaves the first peptide bond.

This cycle can be repeated up to 50 times to identify each amino acid.

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20
Q

What is selective hydrolysis?

A

Cutting the polypeptide chain at specific locations.

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21
Q

What are digestive enzymes?

A

Proteases

22
Q

What does the digestive enzyme trypsin bind and recognize?

A

The amino acids Arg and Lys at the C-terminal, only if Proline is not following it

23
Q

Why does trypsin bind to the C-terminal

A

The carboxylate group is right next to the catalytic unit of trypsin, and a target for hydrolysis.

24
Q

What does the digestive enzyme chymotrypsin act on?

A

The aromatic amino acids: Phe, Tyr, Trp if they are not followed by a Proline.

25
Q

What is Cyanogen Bromide?

A

Chemical reagent

26
Q

What does Cyanogen Bromide attack?

A

It attacks Methionine and converts homoserine

27
Q

What characteristics do proteins digested with enzymes yield?

A

Characteristic patterns of fragments of different molar masses.

28
Q

What can the molar masses of a cut protein be analyzed by?

A

Mass spectrometry - a definitive mean of defining a known protein.

29
Q

How is Mass Spectrometry used to detect protein sequence?

A

1.) Hydrolyze with protease (cut proteins into fragments)
2.) Select one of the fragments to go into collision cell
3.) Measure the fragments masses

30
Q

What will the collision cell fragment each protein into?

A

Into B-type (N-terminus) or Y-type (C-terminus)

31
Q

With trypsin digestion, what will all Y-type fragments be?

A

They will either be Lysine or Arginine and they will be positively charged,

32
Q

What is a Y-Type fragment

A

C-terminal fragment

33
Q

What is the polypeptide backbone formed by?

A

Linked by C-C bonds and C-N bonds

34
Q

What are these single bonds considered to be?

A

Flexible due to bond rotation

35
Q

What shape of bond angles are present in the single bonds?

A

Tertrahedral (109) and Trigonal Planar (120)

36
Q

What is a Conformation?

A

When a molecule can be interconverted by bond rotations without breaking any covalent bonds.

Example: the different shapes of a polypeptide chain

37
Q

What is Configurations?

A

Can only be interchanged by breaking covalent bonds, not bond rotations

Example: Cis and Trans
- Two chiral forms of amino acids.

38
Q

What are X-Ray Diffractions?

A

Using an X-Ray source and X-Ray beams to reflect a deflected beam off a crystal which can be detected by a detector

39
Q

What will a detector do in an X-ray diffraction?

A

The detector can determine major patterns (the dimensions of major patterns can be calculated)

40
Q

What is an example of a Pattern of a protein that was detected by a X-ray diffraction?

A

a-keratin and B-keratin

41
Q

What is the Major and Minor patterns of a-keratin?

A

5.4 A - Major, 1.5 A - Minor

42
Q

What is the Major and Minor patterns of b-keratin?

A

7.0 A - Major, 3.5 A - Minor

43
Q

What did Linus Pauling’s say about the single bonds in a peptide chain?

A

He thought that the single bonds in a peptide chain, were almost too flexible.

44
Q

What was Linus Pauling’s key finding?

A

Even though the peptide bond is a single bond, it has double bond characteristics.

45
Q

What were the bond lengths that Linus Pauling disovered?

A

Normal C - N Bond: 1.49 A

Peptide C - N bond: 1.32 A

Normal C = N bond: 1.27A

46
Q

What did Linus Pauling find about the peptide bond?

A

It is rigid, fixed in trans geometry as it behaves more like a double bond then single bond.

47
Q

What are the two major regular repeating patterns?

A

A helical shape

An extended shape

48
Q

What happens if there is no regular, repeating structure?

A

A random coil - loop or turn

49
Q

What does the helical shape say about bond rotation?

A

Every a-C rotates in the same direction

50
Q

What does the extended shape (beta pleated sheet) say about bond rotation

A

The a-C rotates in opposite directions down the peptide chain

BIOCHEM*2580 (21 decks)

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