Biochem Protein Lecture 1

Question 1

Proteins are polymers of

Answer 1

Amino Acids

Question 2

Each amino acid residue is joined to its neighbor by a specific type of covalent bond:

Answer 2

Peptide Bond

Question 3

How many different amino acids are commonly found in proteins?

Are there many less common ones?

Answer 3

20

Yes

Question 4

What does each amino acid have?

The amino acids differ from each other in their

Answer 4

1) A carboxylic acid group
2) An amino group bonded to the same carbon atom (α carbon)

Side Chains (R-groups

Question 5

Amino acids are grouped into 5 main classes based on their

Answer 5

R-Group Properties

Question 6

Which R-Group property of AAs is particularly important?

Answer 6

Polarity

AAs vary from nonpolar and hydrophobic to polar and hydrophilic

Question 7

This amino acid is the simplest structure of the aliphatic non-polar R-group.

Answer 7

Glycine

Question 8

These nonpolar, alkyl groups tend to cluster together within proteins and stabilize proteins through hydrophobic interactions

Answer 8

Alanine, Valine, Leucine, and isoleucine

Question 9

This amino acid is a non-polar aliphatic and is one of two sulfur containing AAs and has a nonpolar thioether group in its side chain. Note that the electronegativity of sulfur is similar to carbon

Answer 9

Methionine

Question 10

This AA has nonpolar aliphatic side chain with cyclic structure; it’s secondary amino (imino) group is held in rigid conformation, which reduces flexibility of polypeptides containing proline

Answer 10

Proline

Question 11

T/F: Aromatic R groups are relatively nonpolar and hydrophobic

Answer 11

TRUUUUUEEEE

Question 12

This is the 1st aromatic R group

Answer 12

Phenylalanine

Question 13

This aromatic R-Group has a bicyclic ring (indole), it contains an NH group which can form H bonds

Answer 13

Tryptophan

Question 14

This aromatic R-group contains an OH group which can H-bond

Answer 14

Tyrosine

Question 15

Why are tyrosine and tryptophan more polar than phenylalanine?

Answer 15

Because of their H-bonding ability

Question 16

All aromatic aa’s absorb UV light, especially

What absorbance is characteristic of most proteins?

Answer 16

tryptophan

280nm

Question 17

This group of R groups is hydrophilic, contain functional groups that H-bond with water (O and/or N), and the side chains are polar because of large differences in electronegativities between these atoms.

Answer 17

Polar, Uncharged R Groups

Question 18

These polar uncharged R groups contain hydroxyl groups in their side chains

Answer 18

Serine and Threonine

Question 19

This polar uncharged R group contains a sulfhydryl group and is readily oxidized to form a covalently linked dimeric AA called Cystine (two cysteine molecules joined by a disulfide bond)

Disulfide linked residues are strong hydrophilic or hydrophobic?

Answer 19

Cysteine

Hydrophobic (nonpolar)

Question 20

These polar uncharged R groups contain amide groups in their side chains; and differ from each other by a methylene unit (CH2)

Which has an extra methylene unit?

Answer 20

Asparagine and Glutamine

Glutamine

Question 21

Asparagine and glutamine are the ____ of aspartate and glutamate

Answer 21

Amides

Question 22

This group of R groups is very hydrophilic and has a significant positive charge at pH of 7.0

Because they’re basic, they associate with H+ in solution to form positively charged groups

Answer 22

Positively Charged (Basic) groups

Question 23

This positively charged basic R group has a second primary amino group on the epsilon carbon atom

Answer 23

Lysine

Question 24

This positively charged basic R group has a positively charged guanidino group

Answer 24

Arginine

Question 25

This positively charge basic R group has an imidazole group and is the only aa having an ionizable chain with a pKa near neutrality

Answer 25

Histidine

Question 26

The imidazole group of histidine is less or more basic than amino or guanidino groups.

At pH 7, its prredominately unprotonated or protonated

Answer 26

Less

Unprotonated

Question 27

In many enzyme catalyzed reactions, His (histidine) facilitates the reaction by serving as a

Answer 27

Proton donor/acceptor

Question 28

This group of R groups has a net negative charge at pH of 7 and is very hydrophilic

Answer 28

Negatively Charged (Acidic) R groups

Question 29

Both of these negatively charged acidic R groups have a second carboxyl group. They are acidic and dissociate to give H+ and COO- at pH of 7

The carboxyl groups are referred to as beta and gamma carboxyl groups because they’re attached to the beta and gamma carbons

Answer 29

Aspartate

Glutamate

Question 30

Relative to strong acids like HCl and H2SO4, amino acids are

Weak acids undergo ____ over a wide pH range

Answer 30

Weak acids

Question 31

What are the equations for Keq and pKa?

Answer 31

Keq = [H+][A-]/[HA] = Ka

pKa= -log Ka

Question 32

A proton donor and its corresponding proton acceptor make up the

Answer 32

Conjugate acid-base pair

Question 33

what is the example of titration of AA with two ionizible groups
What groups are they

Answer 33

Glycine

COOH and NH3+

Question 34

As pH increases, which group of glycine ionizes first?
Why?

What is the name of the ion form at pH 6 when all of the carboxylic acid has ionized

Answer 34

The carboxylic acid ionizes first because it is a stronger acid than the acid form of amine

Zwitterion Form

Question 35

The pKas of the ionizing groups for glycine are 2.34 for COOH and 9.6 for NH3+. Is this lower or higher than what is typically observed of these groups?

Answer 35

Lower

Question 36

The titration data for glycine shows that glycine has two regions of _______. In these regions, adding base produces relatively small changes in pH

Answer 36

Buffering power

Question 37

This is the only AA providing significant buffering power near neutral pH

Answer 37

Histidine

Question 38

The relationship between an AAs net ____ and the pH of the solution is also obtained from the titration curve

Answer 38

Net Electric Charge

Question 39

At pH 5.97, glycine is present predominately as its dipolar form, does it have a net electric charge?

The characteristic pH at which the net electric charge is zero is called the

Answer 39

No.

Isoelectric Point

Question 40

Note: amino acids with nonionizable R-Groups have similar, though not identical, pKa values

Answer 40

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Question 41

The ratio of the existence of the acidic or basic form of an R group in a solution at a particular pH can be determined from a knowledge of the ____ of the R group and applying the Henderson-Hasselbach equation

What is that equation?

Answer 41

pKa

pH=pKa + log[A-]/[HA]