Chapter 1

Question 1

What is a side chain?

Answer 1

A side chain, or R group, is the part of the amino acid that defines and specifies the various amino acids.

Question 2

What is an amino acid?

Answer 2

An amino acid is a molecule that contains an amino group (-NH2) and a carboxyl group (-COOH).

Question 3

What are the proteinogenic amino acids?

Answer 3

Proteinogenic amino acids are the 20 alpha amino acids encoded by the human genetic code. These are the only amino acids with which you need to have a memorized familiarity.

Question 4

All amino acids are chiral except, _____

Answer 4

glycine

Question 5

Are chiral amino acids L or D?

Answer 5

L

Question 6

What does it mean to be amphoteric?

Answer 6

An amphoteric substance is something that can react like an acid or a base.

Amino acids are amphoteric because the carboxyl group can donate protons and the amino group can accept protons.

Question 7

At low ph, ionizable groups tend to be _______

Answer 7

protonated

Question 8

At high ph, ionizable groups tend to be

Answer 8

deporotonated

Question 9

If the pH is lower than the pKa of a group, then the group will be __________

Answer 9

protonated

Question 10

If the pH is higher than the pKa of a group, then the group will be__________

Answer 10

deprotonated

Question 11

What is a zwitterion?

Answer 11

A zwitterion is a molecule with both a positive and a negative charge simultaneously. This is seen in amino acids at neutral and body pH’s.

Question 12

What will the titration curve of an amino acid look like?

Answer 12

The titration curve of an amino acid will look like the combination of two monoprotic titration curves (or three if the side chain has an ionizable group)

Question 13

What is the isoelectric point (pI)?

Answer 13

Isoelectric point or pI is the pH at which the amino acid is completely neutral as a result of all positive and negative charges balancing out.

Question 14

How does one calculate isoelectric point?

Answer 14

One must take the pKa’s of the functional groups that provide the protein with a +1 and a -1 charge respectively. Then, one simply averages them. For amino acids with no ionizable side chain, this is simply the average of the pKa of the carboxyl group and the pKa of the amino group.

Note, for amino acids with ionizable side chains, it is important to correctly select the 2 pKa’s that correspond to -1 and +1 charge out of the three available pKa’s.

Question 15

Amino acids with acidic side chains have _____ pI’s?

Answer 15

low

Question 16

Amino acids with basic side chains have _____ pI’s?

Answer 16

high

Question 17

What is a peptide?

Answer 17

A peptide is a chain of amino acids.

Question 18

What is a residue?

Answer 18

A residue is just another name for amino acid. It is usually used when referring to amino acids in a peptide.

Question 19

What is an oligopeptide?

Answer 19

An oligopeptide is a relatively small peptide of up to only 20 residues.

Question 20

What is a polypeptide?

Answer 20

A polypeptide is any chain of amino acids that is longer than 20 amino acids.

Question 21

What is a peptide bond?

Answer 21

Peptide bond is just a specific name for the amide bond that holds amino acids together.

Question 22

Peptide Bond Formation occurs via ____________
Remember, dehydration reactions displace a water from the molecules reacting.

Answer 22

condensation aka dehydration

Question 23

What is meant by the term N-terminus?

Answer 23

An N-terminus is the free amino group at the very beginning of a peptide.

Question 24

What is meant by the term C-terminus?

Answer 24

A C-terminus is the free carboxyl group at the very end of a peptide.

Question 25

In what direction are peptides drawn?

Answer 25

Left to right from N-terminus to C-terminus.

Question 26

Describe the strength of the peptide bond.

Answer 26

The peptide bond is resonance stabilized (partial double bond from N lone pair) , and is thus very strong. More often than not, we need to use special enzymes to break these bonds down.

Question 27

What are the four levels of structure seen in proteins?

Answer 27

1. Primary Structure 2. Secondary Structure 3. Tertiary Structure 4. Quaternary Structure

Question 28

What is primary structure and what is its characteristic bond?

Answer 28

Primary structure refers to the actual sequence of amino acids in the protein. These amino acids are held together by peptide bonds.

Question 29

What is secondary structure and what is its characteristic bond?

Answer 29

Secondary structure refers to the formation of repeating patterns of pleated sheets and alpha helices. These patterns are held together by hydrogen bonds between the carboxyl and amino group backbone of the amino acids.

Question 30

What is tertiary structure and what is its characteristic bond?

Answer 30

Tertiary structure refers to the three dimensional folding of the polypeptide chain into its final form. These forms are held together by hydrogen bonds between side chains, salt bridges between positively and negatively charged side chains, and disulfide bonds between cysteine residues.

Question 31

What is quaternary structure?

Answer 31

Quaternary structure refers to the overall structure obtained when two or more separate polypeptides in tertiary structure combine.

Question 32

What is sequencing?

Answer 32

Sequencing is a laboratory technique that allows one to determine the primary structure of a protein. This is most easily done by using the DNA that coded for the protein, although the protein itself can be used if necessary. As you can see below, you can figure out the sequence by trying to replicate the DNA while adding ddnucleotides, which halt replication. For example, if only one nucleotide is produced from the DNA in the ddATP beaker, then I know the first nucleotide in the DNA is A. This can be repeated to get the whole sequence of DNA, which can then be translated into the amino acids present.

Question 33

What is an alpha helix?

Answer 33

An alpha helix is a rodlike structure in which the peptide chain coils clockwise around a central axis. 3.6 residues per turn, H bonds every ten atoms

Question 34

What is a beta pleated sheet?

Answer 34

A beta pleated sheet is a structure in which peptide chains lie alongside one another, forming rows.

Question 35

Describe the special role played by proline in secondary structure

Answer 35

Proline's rigid ring structure makes it unsuitable for inclusion in the middle of alpha helices and beta pleated sheets. When introduced into the middle of these structures, proline produces kinks in the secondary structure. However, proline's rigidity makes it useful at the start of alpha helices and in the turns taken by beta pleated sheets. These are the two locations one is likely to find proline.

Question 36

What are the two main structural classes of proteins?

Answer 36

1. Fibrous Proteins 2. Globular proteins

Question 37

What is a fibrous protein?

Answer 37

A fibrous protein is a protein that resembles long sheets or strands.

Question 38

What is a globular protein?

Answer 38

A globular protein is a protein that is spherical and round

Question 39

During the formation of tertiary structure, hydrophobic amino acids are pushed ___________

Answer 39

into the core

Question 40

What is Cystine?

Answer 40

Cystine is the name used to refer to the disulfide bond made between two cysteine's in a protein.

Question 41

The formation of a disulfide bond is a ________ reaction

Answer 41

oxiduction

Question 42

What is denaturation?

Answer 42

Denaturation is the process by which a protein loses its tertiary structure. This is usually accomplished through disruption of the bonds that hold tertiary structure together.

Question 43

What is a solvation layer?

Answer 43

A solvation layer is a layer formed around a molecule by nearby solvent molecules. These result as a consequence of electrostatic interactions.

Question 44

Why is the pushing of nonpolar amino acids into the core of a protein spontaneous?

Answer 44

When there are nonpolar amino acids on the outside of the protein, water cannot hydrogen bind with the protein, which means it can only hydrogen bind with itself. This reduces water's options, which lowers its entropy, which makes this process unfavorable. On the other hand, if water can hydrogen bind with the outside of the protein (polar AA's on the exterior), that gives water more options and lowers the entropy of the system, which is favorable.

Question 45

What is a subunit?

Answer 45

A sub unit refers to one of the functional tertiary peptides comprising the overall quaternary peptide.

Question 46

What roles can the formation of quaternary structure serve?

Answer 46

1. Quaternary structure can stabilize a protein 2. Quaternary structure can reduce the amount of DNA needed to encode a protein complex 3. Quaternary structure can bring catalytic sites together, which allows intermediates to be shuttled directly to the next step. 4. Quaternary structure can induce cooperativity, also known as allosteric effects.

Question 47

What is a conjugated protein?

Answer 47

A conjugated protein is a protein that derives part of its function from the presence of proesthetic groups.

Question 48

What is a prosthetic group?

Answer 48

A prosthetic group is a covalently attached molecule that allows a protein to function. Prosthetic groups can be organic molecules such as vitamins or metal ions, like iron.

Question 49

What is a lipoproptein?

Answer 49

A lipoprotein is a protein with a lipid based prosthetic group.

Question 50

What is a glycoprotein?

Answer 50

A glycoprotein is a protein with a carbohydrate based prosthetic group.

Question 51

What is a nucleoprotein?

Answer 51

A nucleoprotein is a protein with a nucleotide based prosthetic group.

Question 52

What are common ways to denature a protein?

Answer 52

1. Heat. As temp increases, hydrogen bonds and salt bridges destabilize. 2. Solutes such as urea and beta mercaptoethanol can disrupt disulfide bridges, causing denaturation. 3. Detergents can solubilize proteins, which disrupts noncovalent bonds and therefore promotes denaturation.