7 and 8A Amino acids and Protein Secondary Structure Flashcards

1
Q

How many amino acids do peptides have?

A

50 or less

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

How many amino acids do polypeptides and proteins have?

A

Greater than 50

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are zwitterions?

A

Molecules that have a positive and negative charge, and no net charge at pH 7

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What type of side chains do acidic Amino Acids have?

A

Have a side chain with a carboxylate group that ionizes at physiological pH

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

How are amino acids characterized?

A

Characterized by their ability to interact with water

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

The only non-chiral standard amino acid is?

A

glycine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is the Isoelectric Point (pI)

A

When amino acids have no net charge ue to ionization of both groups

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Peptide bonds are formed by what type of reaction?

A

Amide linkages formed by nucleophilic acyl substitution (dehydration reaction)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

How are Shiff bases formed?

A

By imine products of primary amine groups interacting with carbonyl groups, eg. in amino acid biosynthesis reactions.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is a Schiff base?

A

Referred to as aldimines, are intermediates formed by the reaction of an amino group with an aldehyde group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

How many standard amino acids are there?

A

20

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

How are amino acids amphoteric?

A

They have a carboxyl group which can act as an acid and an amino group that can act as a base

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What are nonpolar amino acids (structurally)?

A

Contain hydrocarbon groups with no charge

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What are polar amino acids?

A

They have functional groups that can easily interact with water through hydrogen bonding.

The functional group is either a hydroxyl group (serine, threonine and tyrosine etc.), thiol group (cysteine) or an amide group (asparigine, glutamine etc.)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is the three and one letter abbreviation of asparigine?

A

ASN

N

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is the three and one letter abbreviation of aspartic acid?

A

Asp

D

17
Q

What is the one letter abbreviation for arginine?

A

R

18
Q

What is the three letter abbreviation for glutamine?

A

Gln

Q

19
Q

What is the three letter abbreviation for isoleucine?

A

Ile

20
Q

What is the three letter abbreviation for tryptophan?

A

Trp

W

21
Q

What are the amino acids involved as metabolic intermediates in the urea cycle?

A

Arginine
Ornithine
Citrulline

22
Q

Which amino acids can be phosphorylated?

A

Serine
Threonine
Tyrosine

23
Q

True or false, amino acids can exist as stereoisomers. Why?

A

True, because the alpha-carbon is attached to four different groups, they can exist as stereoisomers.

(except glycine, which is the only nonchiral standard amino acid)

24
Q

What are D and L used to signify with amino acids?

A

Used to indicate the similarity of the arrangement of atoms around the molecules assymmetric carbon to the asymmetric carbon of the glyceraldehyde isomers (reference compound for optical isomers)

Only L amino acids are used in translation, D can be used after post-translational modifications

25
Q

What causes a more complex titration curve with amino acids?

A

More ionizable side chains cause a more complex titration curve, as it proceeds stepwise as each group is deprotonated by NaOH

26
Q

What are peptide bonds? How are they formed (what type of reaction?)

A

Amide linkages formed by nucleophilic acyl substitution (a dehydration reaction).

27
Q

Where is the free amino group on the peptide chain? Where is the carboxyl group found? What terminal end for each?

A

The N-terminal contains the free amino group, the C-terminal has a free carboxyl group.

28
Q

Is the peptide bond rigid and flat? Or soft and curvy? Why?

A

Rigid and flat (found by Linus Pauling)

The C-N bonds between two amino acids are shorter than other C-N bonds. This gives them partial double bond characteristics (they are resonance hybrids)

29
Q

How many peptide bonds in a polypeptide cannot rotate freely due to their short double-bond-like nature?

A

One third of the bonds in a polypeptide backbone cannot rotate freely.

This limits the number of conformational possibilities

30
Q

What happens when cysteine is oxidized?

A

A reversible disulphide bridge between another oxidized cysteine

31
Q

What does a cysteine-cysteine disulfide double bridge do for the polypeptide?

A

Helps stabilize it

32
Q

When do Shiff base formations occur most? (most importantly)

A

Amino acid biosynthesis reactions