Lecture 4 Amino Acids and Proteins

Question 1

How many standard amino acids are there?

Answer 1

20

Question 2

How are the 20 standard amino acids similar and different?

Answer 2

20 standard amino acids share a typical structure but differ in their side chains

Question 3

What do peptide bonds do in a polypeptide?

Answer 3

Link amino acid residues

Question 4

Some amino acid side chains contain…..

Answer 4

….ionizable groups whose pK
values may vary

Question 5

What are all proteins composed of?

Answer 5

20 Standard amino acids

Question 6

What are the common amino acids known as?

Answer 6

α-amino acids

Question 7

Why are the common amino acids are known as α-amino acids?

Answer 7

They have a primary amino group (—NH2) as a substituent of the α carbon atom, the carbon next to the carboxylic acid group

Question 8

At physiological
pH …..

Answer 8

…. the amino group is protonated and the
The carboxylic acid group is unprotonated

Question 9

Describe condensation of two amino acids

Answer 9

Formation of a CO—NH bond
with the elimination of a
water molecule produces a
dipeptide.

Question 10

What is the residue of condensation of 2 amino acids?

Answer 10

The residue with a free amino group is the N-terminus of the peptide, and the residue with a free carboxylate group is the C-terminus.

Question 11

Amino acid side chains can be (name 3 things) ?

Answer 11

Nonpolar, Polar, or Charged

Question 12

Name the non polar amino acids

Answer 12

Gly, Ala, Val, Leu,
Ile, Met, Pro, Phe, Trp

Question 13

Name the uncharged polar amino acids

Answer 13

Ser, Thr, Asn, Gln, Tyr, Cys

Question 14

Name the charged amino acids

Answer 14

Lys, Arg, His, Asp, Glu

Question 15

Name the Aliphatic amino acids

Answer 15

Alanine, Valine, Leucine, Isoleucine, Proline

Question 16

Name the - charged amino acids

Answer 16

Aspartic acid, Glutamic acid

Question 17

Name the + charged amino acids

Answer 17

Lysine, Arginine, Histidine

Question 18

Name the aromatic amino acids

Answer 18

Phenylalanine, Tryptophan, Tyrosine

Question 19

Name the amidic amino acids

Answer 19

Asparagine, Glutamine,

Question 20

Name the hydroxylic amino acids

Answer 20

Serine, Threonine

Question 21

Name the sulfur containing amino acids

Answer 21

Cysteine, Methionine

Question 22

Watch the lecture recording to make notes on Classifying Amino Acids p6

Answer 22

Yes, do that Nadya

Question 23

What do the pK Values depend on?

Answer 23

The pK Values of Ionizable Groups Depend on Nearby Groups

Question 24

What is the isoelectric point (pI) for the α-amino acids?

Answer 24

The pH at which a molecule carries no net electric charge is known as its
isoelectric point, pI.

Question 25

What is the formula for calculating pl?

Answer 25

pI = 1/2(pKi + pKj)

Question 26

What are the Ki and Kj in this calculation?

Answer 26

Ki and Kj are the dissociation constants of the two ionizations involving the neutral species

Question 27

Calculate the isoelectric point of aspartic acid. In the neutral species, the α-carboxylate group is
deprotonated, and the α-amino group is protonated. Protonation of the α-carboxylate group or deprotonation of the
β-carboxylate group would both yield charged species. Therefore, the pK values for these groups (1.99 and 3.90)

Answer 27

pI = (pKi + pKj)/2
= (1.99 + 3.90)/2 = 2.9

Question 28

Amino acids and many other biological compounds are…..

Answer 28

,,,,chiral molecules
whose configurations can be depicted by Fischer projections

Question 29

The amino acids in proteins all have what configuration?

Answer 29

L stereochemical configuration

Question 30

All the amino acids recovered from polypeptides are optically active except which one?

Answer 30

Glycine

Question 31

What does optically active mean?

Answer 31

They rotate the plane
of polarized light

Question 32

What can the direction and angle of rotation be measured with?

Answer 32

An instrument
known as a polarimeter

Question 33

The central atoms in such molecules are known as….

Answer 33

…asymmetric or chiral centers and are said to have the property of chirality

Question 34

What is the Fischer convention?

Answer 34

The Fischer Convention Describes the Configuration of Asymmetric Centers.

Question 35

In the Fischer convention….

Answer 35

…..horizontal bonds extend above the plane of the paper, and vertical bonds extend below the plane of the article

Question 35

Are the 20 standard amino acids the only amino acids that occur in biological
systems?

Answer 35

No

Question 35

Nonstandard amino acid residues are often important constituents of what?

Answer 35

Proteins and
biologically active peptides

Question 36

The non-standard amino acids are a result of what?

Answer 36

The specific modification of an amino acid residue after the synthesized polypeptide chain

Question 37

What does amino acids modification include?

Answer 37

The simple addition of small chemical groups to specific amino acid side chains

Question 38

Name amino acid modification processes (5)

Answer 38

Hydroxylation, methylation, acetylation, carboxylation, and phosphorylation

Question 39

At neutral pH, the amino group of an amino acid is ______ , and its carboxylic acid group is _________

Answer 39

1. Protonated
2. Ionized

Question 40

What are proteins?

Answer 40

Proteins are polymers of amino acids joined by peptide bonds.

Question 41

When can the pK values of the ionizable groups of amino acids be altered?

Answer 41

When the amino acid is part of a polypeptide

Question 42

Amino acids are -_____ molecules

Answer 42

Chiral molecules

Question 43

Only what acids occur in proteins ? (mention the exception)

Answer 43

Only L-amino acids occur in proteins (some
bacterial peptides contain D-amino acids)

Question 44

How can amino acids be modified ?

Answer 44

Covalently modified after they have been incorporated into a polypeptide

Question 45

What is the size and composition of polypeptide chains limited by in a cell?

Answer 45

By the efficiency of protein synthesis and by the ability of the polypeptide to fold into a functional structure

Question 46

What is a protein’s primary structure?

Answer 46

The amino acid sequence of its polypeptide chain, or chains if the protein consists of more than one polypeptide

Question 47

Except glycine, all the amino acids recovered from polypeptides are what?

Answer 47

Optically active; they rotate the plane of polarized light

Question 48

What can the direction and angle of rotation be measured with?

Answer 48

Polarimeter

Question 49

The central atoms in such molecules are known as what?

Answer 49

Asymmetric or chiral centers and are said to have the property of chirality

Question 50

What does the Fischer Convention Describe?

Answer 50

The Configuration of Asymmetric Centers

Question 51

In Fischer Convention, the configuration of the groups around an asymmetric center is compared to what?

Answer 51

Glyceraldehyde, a molecule with one asymmetric center

Question 52

In the Fischer conventions how are the bonds represented?

Answer 52

Horizontal bonds extend above the plane of the paper, and vertical bonds extend below the plane of the article

Question 53

Higher levels of protein structure—secondary, tertiary, and quaternary refer to what?

Answer 53

To the three-dimensional shapes of folded polypeptide chains

Question 54

A relatively small protein molecule may consist of a single polypeptide chain of
___ residues.

Answer 54

100

Question 55

How many possible unique polypeptide chains of this
length are there?

Answer 55

100 130
20 ≈ 1.27 × 10

Question 56

Forty residues appear to be near the minimum for a polypeptide chain to do what?

Answer 56

To fold into a discrete and stable shape that allows it to carry out a particular function

Question 57

The longer the polypeptide….

Answer 57

….the greater the likelihood of introducing errors during transcription and translation

Question 58

The solubility of a protein at low ion concentrations ______ as salt is added

Answer 58

increases