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Biocheem > Lecture 12 > Flashcards

Lecture 12 Flashcards

1
Q

What is the charge of Lysine at pH 7?

A

It is positively charged because of the amino group in the side chain

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2
Q

What does the side chain of Lysine contain?

A

A positively charged side chain

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3
Q

What kind of H bonds is the side chain of Lysine capable of forming?

A

It is an H-bond donor through its amino group at neutral pH’s

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4
Q

What is the Polarity of Lysine?

A

It is very polar

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5
Q

What is the pKa of the amino group in the R group of Lysine?

A

It has a pKa of 10

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6
Q

What charge does Lysine have at pH 7?

A

A positive charge

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7
Q

Why does Lysine have a positive charge at pH 7?

A

Because it has an NH3 group

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8
Q

Why is Lysine know as a basic amino acid?

A

Because it exists as a base at neutral pH through it amino group

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9
Q

What is the charge of Arginine at pH 7?

A

It is positively charged

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10
Q

What is a Guanido group?

A

The end part of the R group of arginine

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11
Q

What is the pKa of the NH2 of Arginine?

A

12.5

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12
Q

Why is it difficult to deprotonate the functional group of Arginine?

A

Because it is very stable due to resonance

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13
Q

Why can Arginine be described as a basic amino acid?

A

Because the side chain is neutral when it is in the base form

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14
Q

What is the polarity of arginine?

A

It is very polar

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15
Q

What is the H-bond capability of Arginine?

A

It is an H-bond donor

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16
Q

What are the exceptions for the amino acid abbreviation rules?

A
  • Asparagine (Asn)
  • Glutamine (Gln)
  • Isoleucine (Ile)
  • Tryptophan (Trp)
17
Q

Where are Polar side chains usually found?

A

In proteins on the surface where they can interact with water

18
Q

Where are non-polar side chains usually found?

A

Buried in the protein core to minimize interaction with water

19
Q

Which parts of the amino acid is a peptide bond between?

A

The carboxyl of one amino acid and the amino group of another amino acid

20
Q

What is removed in the formation of a peptide bond?

A

Two H’s from the amino group and one O from the carboxyl group to form a water

21
Q

What is the symmetry of the bond that connects amino acids together?

A

It is asymmetrical

22
Q

What does the N-terminal describe?

A

The presence of a free amino group

23
Q

What does the C-terminal describe?

A

The presence of a C terminal on one end

24
Q

What is a Dipeptide, Tripeptide, Tetrapeptide, Pentapeptide?

A

Two amino acids, three amino acids, four amino acids, five amino acids

25
Q

What is an Oligopeptide?

A

The general term for a larger number of amino acids, often refers to synthetic. peptides

26
Q

What is a Polypeptide?

A

A long chain of amino acids, usually produced naturally

27
Q

What is a Protein?

A

A large polypeptide a with a biological function

28
Q

What retains their charge in a peptide?

A
  • Terminal amino group (+1)
  • Carboxylate group (-1)
  • Side chains (if they have one)
29
Q

How are the number of connected amino acids related to the peptide bond?

A

There will always be one less peptide bond than amino acids

30
Q

What is the Primary Structure?

A

The sequence of amino acids in a polypeptide

31
Q

What joins each amino acid to the next?

A

A covalent peptide bond

32
Q

From which terminus do we read polypeptide chains?

A

From N-terminus to C-terminus

33
Q

Where is no rotation permitted in peptide bonds?

A

Rotation is not permitted around the C-N bond because of the double bond character

34
Q

In a peptide bond, which atoms are found in the same plane?

A
  • Two Alpha carbons
  • Carbonyl carbon
  • Oxygen
  • Nitrogen
  • Hydrogen on the nitrogen
35
Q

What are the three kinds of bonds in a peptide bond?

A
  • N - Calpha
  • Calpha - carbonyl carbon
  • Carbonyl carbon - nitrogen
36
Q

Which bonds in a peptide bond allow for rotation?

A

N - Calpha and C-alpha to Carbon of the carbonyl

37
Q

What does the Primary structure determine?

A

The 3D structure

38
Q

Why is the folding conformations of polypeptides limited?

A

Due to steric hindrance

39
Q

What is the hydrogen bonding potential of a peptide bond?

A

The carbonyl and N-H can hydrogen bond with each other

Biocheem (38 decks)

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