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MCAT Biochemistry > Chapter 1: Amino Acids, Peptides, and Proteins > Flashcards

Chapter 1: Amino Acids, Peptides, and Proteins Flashcards

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MCAT flashcards
1
Q

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

A

Amino Acids

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2
Q

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.

A

α-amino-acids

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3
Q

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.

A

R group (Side Chain)

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4
Q

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

A

Proteinogenic Amino Acids

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5
Q

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.

A

Glycine, Gly, G

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6
Q

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.

A

Cysteine, Cys, C

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7
Q

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

A

L-amino-acids

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8
Q

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

A

Alanine, Ala, A

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9
Q

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

A

Valine, Val, V

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10
Q

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

A

Leucine, Leu, L

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11
Q

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

A

Isoleucine, Ile, I

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12
Q

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.

A

Methionine, Met, M

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13
Q

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.

A

Proline, Pro, P

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14
Q

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

A

Tryptophan, Trp, W

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15
Q

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.

A

Phenylalanine, Phe, F

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16
Q

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.

A

Tyrosine, Tyr, Y

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17
Q

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.

A

Serine, Ser, S

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18
Q

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.

A

Threonine, Thr, T

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19
Q

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.

A

Asparagine, Asn, N

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20
Q

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.

A

Glutamine, Gln, Q

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21
Q

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.

A

Thiol

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22
Q

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.

A

Aspartic acid, Asp, D

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23
Q

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.

A

Glutamic acid, Glu, E

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24
Q

The depronated form or anion of Aspartic Acid.

A

Aspartate

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25
Q

The depronated form or anion of Glutamic Acid.

A

Glutamate

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26
Q

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

A

Lysine, Lys, K

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27
Q

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.

A

Arginine, Arg, R

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28
Q

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.

A

Histidine, His, H

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29
Q

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.

A

Amphoteric Species

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30
Q

________ 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.

A

Ionizable Groups

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31
Q

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.

A

pKa

32
Q

This value is known as the physiological pH.

A

7.4

33
Q

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

A

Zwitterions (Dipolar Ions)

34
Q

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

A

Isoelectric Point (pI)

35
Q

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

A

Done by averaging the two pKa values for the amino and carboxyl groups

36
Q

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

A

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

37
Q

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

A

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

38
Q

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

A

Peptides

39
Q

These consist of two amino acid residues.

A

Dipeptides

40
Q

These consist of three amino acid residues.

A

Tripeptides

41
Q

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

A

Oligopeptides

42
Q

This term is used to describe long peptide chains of residues

A

Polypeptides

43
Q

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)

A

Peptide Bonds
-C(O)NH-

44
Q

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

A

Condensation and/or Dehydration

45
Q

Why can amide groups exhibit resonance?

A

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.

46
Q

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

A

A-terminus (amino terminus)

47
Q

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

A

C-terminnus (Carboxyl terminus)

48
Q

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

A

N-terminus on left
C-terminus on right

49
Q

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

A

Trypsin

50
Q

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

A

Chymotrypsin

51
Q

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

A

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

52
Q

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.

A

Proteins

53
Q

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.

A

Primary (1°)

54
Q

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.

A

Sequencing

55
Q

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.

A

Secondary (2°)

56
Q

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.

A

α-Helix

plural is α-Helices

57
Q

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

A

Keratin

58
Q

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.

A

β-Pleated Sheets

59
Q

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

A

Fibrion

60
Q

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

A

Fibrous Proteins

61
Q

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

A

Globular Proteins

62
Q

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.

A

Tertiary (3°)

63
Q

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.

A

Disulfide Bonds

64
Q

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.

A

Protein Folding

65
Q

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

A

Denaturation

66
Q

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

A

Solvation Layer

67
Q

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.

A

Quarentary (4°)

Examples include Hemoglobin and Immunoglobin structures

68
Q

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

A

Cooperativity (Allosteric Effects)

69
Q

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

A

Conjugated Proteins

70
Q

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

A

Prosthetic Groups

71
Q

Proteins with lipid prosthetic groups

A

Lipoproteins

72
Q

Proteins with carbohydrate prosthetic groups

A

Glycoproteins

73
Q

Proteins with nucleic acid prosthetic groups

A

Nucleoproteins

74
Q

Why are proteins denatured by heat?

A

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

75
Q

Why are proteins denatured by solutes?

A

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

MCAT Biochemistry (5 decks)

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