Chapter 1: Amino Acids, Peptides, and Proteins

Question 1

Molecules that contain two functional groups: an amino group (-NH2) and a carbonyl group (-COOH)

Answer 1

Amino Acids

Question 2

The amino group and the carbonyl group are bonded to the same carbon to form this molecule. The carbon is known as the α-carbon of the carbonyl group.

Answer 2

α-amino-acids

Question 3

Along with a hydrogen atom, this specific group is attached to the α-carbon. It is specific to each amino acid and determines the properties of amino acids, and therefore their functions.

Answer 3

R group (Side Chain)

Question 4

20 α-amino-acids encoded by the human genetic code.

Answer 4

Proteinogenic Amino Acids

Question 5

One of seven amino acids that are nonpolar and nonaromatic. The only amino acid that is achiral, meaning that it has a hydrogen atom as its R group. This amino acid is also the smallest amino acid.

Answer 5

Glycine, Gly, G

Question 6

One of two amino acids with a Sulfur. One of five amino acids that have a polar side chain but are not aromatic. The only L-amino-acid that has an (R) absolute configuration instead of an (S) absolute configuration due to the -CH2SH group having priority over the -COOH group.

Answer 6

Cysteine, Cys, C

Question 7

All chiral amino acids used in eukaryotes are __________, so the amino group is drawn on the left in a Fischer projection.

Answer 7

L-amino-acids

Question 8

One of seven amino acids that are nonpolar and nonaromatic. Has an akyl side chain containing one carbon.

Answer 8

Alanine, Ala, A

Question 9

One of seven amino acids that are nonpolar and nonaromatic. Has an akyl side chain containing three carbons.

Answer 9

Valine, Val, V

Question 10

One of seven amino acids that are nonpolar and nonaromatic. Has an akyl side chain containing four carbons.

Answer 10

Leucine, Leu, L

Question 11

One of seven amino acids that are nonpolar and nonaromatic. Has an akyl side chain containing four carbons.

Answer 11

Isoleucine, Ile, I

Question 12

One of only two amino acids that contains a sulfur atom in its side chain. Still considered non-polar becuase the sulfur has a methyl group attached to it. Nonpolar and nonaromatic.

Answer 12

Methionine, Met, M

Question 13

One of seven amino acids that are nonpolar and nonaromatic. The only amino acid that is formed cyclic. This is due to the amino nitrogen becoming a part of the side chain forming a five-membered ring. This also makes it less flexible.

Answer 13

Proline, Pro, P

Question 14

One of three amino acids with an uncharged aromatic side chain. The largest one with a double-ringed system containing a nitrogen.

Answer 14

Tryptophan, Trp, W

Question 15

One of three amino acids with an uncharged aromatic side chain. The smallest one with a benzyl side chain (a benzene ring plus a -CH2-group). Relativley nonpolar.

Answer 15

Phenylalanine, Phe, F

Question 16

One of three amino acids with an uncharged aromatic side chain. Similar structure to phenylalanine but with the adidtion of a -OH group that makes it polar.

Answer 16

Tyrosine, Tyr, Y

Question 17

One of five amino acids that have a polar side chain but are not aromatic. Has an -OH group side chain allowing it to be highly polar and participate in hydrogen bonding.

Answer 17

Serine, Ser, S

Question 18

One of five amino acids that have a polar side chain but are not aromatic. Has an -OH group side chain allowing it to be highly polar and participate in hydrogen bonding.

Answer 18

Threonine, Thr, T

Question 19

One of five amino acids that have a polar side chain but are not aromatic. Has an amide side chain. Unlike the amino group common to all amino acids, the amide nitrogens do NOT gain or lose electrons with changes to pH; they do not become charged.

Answer 19

Asparagine, Asn, N

Question 20

One of five amino acids that have a polar side chain but are not aromatic. Has an amide side chain. Unlike the amino group common to all amino acids, the amide nitrogens do NOT gain or lose electrons with changes to pH; they do not become charged.

Answer 20

Glutamine, Gln, Q

Question 21

The name of the (-SH) group iun the side chain of cysteine. This bond is longer and weaker than an O-H bond as well as more electronegative making cysteine prone to oxidation.

Answer 21

Thiol

Question 22

One of two amino acids that can have a negative charge on its side chain when depronated. Has a carboxylate group (-COO-) in its side chain.

Answer 22

Aspartic acid, Asp, D

Question 23

One of two amino acids that can have a negative charge on its side chain when depronated. Has a carboxylate group (-COO-) in its side chain.

Answer 23

Glutamic acid, Glu, E

Question 24

The depronated form or anion of Aspartic Acid.

Answer 24

Aspartate

Question 25

The depronated form or anion of Glutamic Acid.

Answer 25

Glutamate

Question 26

One of three amino acids that have side chains containing positively charged nitrogen atoms. Has a terminal primary amino group.

Answer 26

Lysine, Lys, K

Question 27

One of three amino acids that have side chains containing positively charged nitrogen atoms. Has three nitrogen atoms in its side chain; the positive charge is delocalized over all three nitrogen atoms.

Answer 27

Arginine, Arg, R

Question 28

One of three amino acids that have side chains containing positively charged nitrogen atoms. Has an aromatic ring with two nitrogen atoms (the ring is called an imidazole). The positive charge here is due to its pH being close to the physiological pH of 7.4 leading one nitrogen to be pronated and the other is not.

Answer 28

Histidine, His, H

Question 29

Amino acids have both an acidic carboxylic acid group and a basic amino group which makes them known as ________. This means that they can either accept a proton or donate a proton.

Answer 29

Amphoteric Species

Question 30

________ tend to gain protons under acidic conditions and lose them under basic conditions. So in general, they tend to be pronated at low pH and depronated at high pH.

Answer 30

Ionizable Groups

Question 31

The ____ of a group is the pH at which, on average, half of the molecules of that species are depronated. If the pH is less than this value than the majority of the species will be pronated. If the pH is higher however, than the majority of the species will be depronated.

Answer 31

p*K*a

Question 32

This value is known as the physiological pH.

Answer 32

7.4

Question 33

A molecule that has both a positive and a negative charge but overall is electrically neutral.

Answer 33

Zwitterions (Dipolar Ions)

Question 34

For all amino acids, this is the terms used to describe the pH when the molecule is electrically neutral.

Answer 34

Isoelectric Point (pI)

Question 35

The equation to calculate the isoelectric point (pI) of neutral amino acids.

Answer 35

Done by averaging the two p*K*a values for the amino and carboxyl groups

Question 36

The equation to calculate the isoelectric point (pI) of acidic amino acids (or amino acids with charged side chains)

Answer 36

Done by averaging the pKa values of the carboxyl group and the side chain (R group)

Question 37

The equation to calculate the isoelectric point (pI) of basic amino acids.

Answer 37

Done by averaging the pKa values of the amino group and the side chain (R group)

Question 38

These are composed of amino acid subunits that are sometimes called residues.

Answer 38

Peptides

Question 39

These consist of two amino acid residues.

Answer 39

Dipeptides

Question 40

These consist of three amino acid residues.

Answer 40

Tripeptides

Question 41

This term is used to describe relatively small peptides, up to about 20 residues.

Answer 41

Oligopeptides

Question 42

This term is used to describe long peptide chains of residues

Answer 42

Polypeptides

Question 43

A specialized form of an amide bond, which form between the -COO- group of one amino acid and the NH3+ group of another amino acid. (Give bond name and functional group formed)

Answer 43

Peptide Bonds -C(O)NH-

Question 44

Peptide bond formation is an example of a ________ and/or ________ reaction because of the removal of a water molecule (H2O).

Answer 44

Condensation and/or Dehydration

Question 45

Why can amide groups exhibit resonance?

Answer 45

Because they have delocalizable π (pi) electrons in the carbonyl and in the lone pair on the amino nitrogen, thus leading to the C-N bond in the amide having a partial double bond character.

Question 46

When a peptide bond is formed, the free amino end is known as the ________.

Answer 46

A-terminus (amino terminus)

Question 47

When a peptide bond is formed, the free carboxyl end is known as the ________.

Answer 47

C-terminnus (Carboxyl terminus)

Question 48

By convention, peptides are drawn and read with the ____ on the left and the ____ on the right.

Answer 48

N-terminus on left C-terminus on right

Question 49

A hydrolytic enzyme in living organisms that cleaves at the carboxyl end of arginine and lysine.

Answer 49

Trypsin

Question 50

A hydrolytic enzyme in living organisms that cleaves at the carboxyl end of phenylalanine, tryptophan, and tyrosine.

Answer 50

Chymotrypsin

Question 51

How do hydrolyic enzymes catalyze hydrolysis in living organisms? (give main idea, not exact mechanism)

Answer 51

The break apart the amide bond by adding a hydrogen atom to the amide nitrogen and an OH group to the carbonyl carbon. | The reverse reaction of peptide formation, figure 1.10 in book

Question 52

Polypeptides that range from just few amino acids in length up to thousands. They serve many functions like enzymes, hormones, membrane pore and receptors, and elements of cell structure.

Answer 52

Proteins

Question 53

One of four protein struction levels, characterized by being the linear arrangement of amino acids encoded in an organisms DNA: the sequence of amino acids. Stabilized by the formation of covalent peptide bonds between adjacent amino acids.

Answer 53

Primary (1°)

Question 54

The technique done in laboratories to determine the primary structure of an protein. Done by using the protein itself or the DNA that coded for it.

Answer 54

Sequencing

Question 55

One of four protein struction levels. Referred to as the local structure of neighboring amino acids. These strucutures are primarily the result of hydrogen bonding between nearby amino acids.

Answer 55

Secondary (2°)

Question 56

A rod-like structure in which the peptide chain coils clockwise around a central axis. This structure is stabilized by intramolecular hydrogen bonds between a carbonyl oxygen atom and an amide hydrogen atom four residues down the chain. Also an important component in the structure of Keratin.

Answer 56

α-Helix | plural is α-Helices

Question 57

A fibrous structural protein found in human skin, hair, and fingernails.

Answer 57

Keratin

Question 58

Formation of peptide chains that lie alongside one another, forming rows or strands held together by intramolecular hydrogen bonds between carbonyl oxygen atoms on one chain and amide hydrogen atoms in an adjacent chain.

Answer 58

β-Pleated Sheets

Question 59

The primary protein component of silk fibers that is composed of β-pleated sheets

Answer 59

Fibrion

Question 60

Proteins, such as collagen, that have stuctures that resemble sheets or long strands

Answer 60

Fibrous Proteins

Question 61

Proteins, such as myoglobin, that tend to be spherical (globe-like)

Answer 61

Globular Proteins

Question 62

One of four protein struction levels. Characterized as the protein's three-dimensional shape. Mostly determined by hydrophilic and hydrophobic interactions between R groups of amino acids.

Answer 62

Tertiary (3°)

Question 63

A particularly important component of teriary structure is the presence of ____, these form when two cysteine molecules become oxidized to form cystine. This component also is responsible for creating loops in the protein chain.

Answer 63

Disulfide Bonds

Question 64

A basic idea that secondary structures probably form first, and then the hydrophobic interactions and hydrogen bonds cause the protein to "collapse" into its proper three-dimensional structure. A rapid process where along the way, the adoption of intermediate states called molten globules form.

Answer 64

Protein Folding

Question 65

The process of a protein losing its three-dimensioonal structure and function. Often but not always irreversible

Answer 65

Denaturation

Question 66

This forms around the solute whenever that solute dissolves in a solvent an the nearby molecules come together.

Answer 66

Solvation Layer

Question 67

One of four protein struction levels. Unlike the other three, not all proteins have this structure. These structures only exist for proteins that contain more than one polypeptide chain. The structure is an aggregate of smaller globular peptides, or subunits, and represents the functional form of a protein.

Answer 67

Quarentary (4°) | Examples include Hemoglobin and Immunoglobin structures

Question 68

Basic idea that one subunit can undergo conformational or structural changes, which either enchance or reduce the activity of the other subunits.

Answer 68

Cooperativity (Allosteric Effects)

Question 69

Proteins that derive part of their function from covalently attached molecules called prosthetic groups.

Answer 69

Conjugated Proteins

Question 70

Can be organic molecules such as vitamins, or even metal ions, such as iron. Help conjuagted proteins derive a function.

Answer 70

Prosthetic Groups

Question 71

Proteins with lipid prosthetic groups

Answer 71

Lipoproteins

Question 72

Proteins with carbohydrate prosthetic groups

Answer 72

Glycoproteins

Question 73

Proteins with nucleic acid prosthetic groups

Answer 73

Nucleoproteins

Question 74

Why are proteins denatured by heat?

Answer 74

Heat denatures proteins by increasing their average kinetic energy thus disrupting hydrophobic interactions

Question 75

Why are proteins denatured by solutes?

Answer 75

Solutes denature proteins by disrupting elements of secondary, tertiary, and quarentary structure.