Biochemistry Ch. 1

Question 1

List the aromatic amino acids

Answer 1

1) Phenylalanine
2) Tryptophan
3) Tyrosine

Question 2

List the acidic amino acids

Answer 2

1) Aspartic acid

2) Glutamic acid

Question 3

List the basic amino acids

Answer 3

1) Arginine
2) Histidine
3) Lysine

Question 4

List the aliphatic amino acids

Answer 4

1) Alanine
2) Glycine
3) Isoleucine
4) Leucine
5) Proline
6) Valine

Question 5

List the hydroxylic amino acids

Answer 5

1) Serine

2) Threonine

Question 6

List the sulfur-containing amino acids

Answer 6

1) Cysteine

2) Methionine

Question 7

List the amidic amino acids

Answer 7

1) Asparagine

2) Glutamine

Question 8

List the essential amino acids

Answer 8

1) Isoleucine
2) Leucine
3) Valine
4) Phenylalanine
5) Tryptophan
6) Histidine
7) Lysine
8) Serine
9) Threonine

Question 9

___ side chains have high pI’s while ___ side chains have low pI’s

Answer 9

Basic, acidic

Question 10

What is a peptide bond?

Answer 10

Condensation/dehydration/acyl substitution/type of amide bond that forms between the COO- and NH+ group of two amino acids to form a -C(O)NH- group

Question 11

How do trypsin and chymotrypsin catalyze hydrolysis?

Answer 11

Break apart amide bond by adding H to amide N and OH to carbonyl C

Question 12

The __ terminus is the amino end

Answer 12

N

Question 13

The __ terminus is the carboxyl end

Answer 13

C

Question 14

Define primary protein structure

Answer 14

A linear arrangement of amino acids that is stabilized by the peptide bonds between adjacent amino acids

Question 15

___ protein structure has no subtypes

Answer 15

primary

Question 16

Define secondary protein structure

Answer 16

A local structure of neighboring amino acids stabilized by intramolecular H bonding between different residues of amino acids

Question 17

List the two subtypes of secondary protein structures

Answer 17

Alpha helix and beta sheet

Question 18

Define alpha helix

Answer 18

A secondary protein structure of a peptide chains and side chains

Question 19

Describe the structure of an alpha helix

Answer 19

Coil of peptide chains, side chains point away from core, H bond is formed between residues of the same peptide

Question 20

Define beta sheet

Answer 20

A secondary protein structure of parallel and antiparallel rows of peptide chains

Question 21

Describe the structure of a Beta sheet

Answer 21

Parallel and antiparallel rows of peptide chains, R groups point above and below the plane, H bonds are formed between residues of different peptide chains

Question 22

A beta sheet has H bonds formed between residues of ___ peptide chains

Answer 22

Different

Question 23

An alpha helix has H bonds formed between residues of ___ peptide chains

Answer 23

Same

Question 24

How does proline affect the secondary structure of a protein?

Answer 24

Introduces kink in alpha helix and turn in beta sheet

Question 25

Where is proline typically found in a secondary protein structure?

Answer 25

In the turns between chains of beta sheets and as reside at start of alpha helix

Question 26

List the types of proteins

Answer 26

1) Fibrous

2) Globular

Question 27

What stabilizes/forms tertiary structures?

Answer 27

1) The shuffling of hydrophobic side groups to the inner core of a protein and the shuffling of hydrophilic groups (N-H and C=O) to the outside
2) Disulfide bonds between cysteine molecules
3) Salt bridges between amino acids with charged R groups

Question 28

Define solvation layer

Answer 28

The organization of solvent around solute

Question 29

Salt bridges form between ___

Answer 29

Amino acids with charged R groups

Question 30

Cystine is formed from what? what type of reaction is this?

Answer 30

From the disulfide bonds between two cysteine molecules

Oxidation reaction

Question 31

Quaternary structures only occur when?

Answer 31

For proteins with more than 1 polypeptide chain

Question 32

List the functions of forming a quaternary protein structure:

Answer 32

1) Stabilizes protein by reducing surface area
2) Reduces amount of DNA needed to encode protein complex
3) Bring catalytic sites closer together so intermediates from 1 reaction can be directly shuttled to 2nd reaction
4) Induce cooperativity/allosteric effects

Question 33

Conjugated proteins have ___ly attached ___ groups

Answer 33

Covalently attached; prosthetic

Question 34

List the conjugated proteins and their prosthetic groups

Answer 34

1) Lipoproteins: have lipid as prosthetic group
2) Glycoproteins: have carbohydrate as prosthetic group
4) Nucleoproteins: have nucleic acid as prosthetic group

Question 35

___ proteins can’t catalyze reactions

Answer 35

Unfolded

Question 36

List the 2 main causes of denaturation

Answer 36

1) Heat

2) Solutes

Question 37

How can heat cause denaturation of a protein?

Answer 37

Breaks hydrophobic interactions holding protein together

Question 38

How can solutes cause protein denaturation?

Answer 38

Directly interfere with the forces holding a protein together (i.e. break disulfide bridges and side chain interactions on alpha helices and beta sheets)

Question 39

How do you determine the pI value of an amino acid with a non-ionizable side chain?

Answer 39

Average the pka values of the terminal alpha carboxyl and amino groups

Question 40

How do you determine the pI value of an amino acid with an ionizable and acidic side chain?

Answer 40

Average the pka values of ther terminal alpha carboxyl group and the side chain

Question 41

Define isoelectric point

Answer 41

The point at which the positive and negative charges on a protein are equal so that the net charge is zero

Question 42

How do you determine the pI of an amino acid with a basic side chain?

Answer 42

Average the pka values of the terminal alpha amino group and the side chain

Question 43

How do you determine the pI of an amino acid with a side chain that is ionizable but neither basic nor acidic?

Answer 43

Determine the median pka value is (of the pka values of the terminal alpha carboxyl group, terminal alpha amino group, and side chain) and add it with the pka value of the terminal alpha carboxyl group, then average it (divide by 2)

Question 44

If the pH of solution is greater than the pKa, the group is in the ____ form.

Answer 44

conjugate base form (deprotonated).

Question 45

If the pH of solution is less than the pKa, the group is in the ___ form

Answer 45

conjugate acid form (protonated).