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Biochemistry Flashcards

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1
Q

Amino acids

A

Molecules that contain an a amino group, a carboxyl group, a hydrogen atom, and a side chain/R group

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2
Q

Side chain/R group

A

Specific to each amino acid

Determines the properties and functions of amino acids

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3
Q

Proteinogenic amino acids

A

The 20 a-amino acids encoded by the human genetic code

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4
Q

What are the proteinogenic amino acids?

A

Alanine, Arginine, Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glutamine, Glycine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Proline, Serine, Threonine, Tryptophan, Tyrosine, and Valine

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5
Q

Glycine, Gly, G

A

Smallest amino acid
Only achirl amino acid
Nonpolar, nonaromatic side chain
Has H as its R group

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6
Q

Alanine, Ala, A

A

Nonpolar, nonaromatic side chain

1 carbon alkyl side chain

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7
Q

Valine, Val, V

A

Nonpolar, nonaromatic side chain

3 carbon alkyl side chain

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8
Q

Leucine, Leu, L

A

Nonpolar, nonaromatic side chain

4 carbon alkyl side chain

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9
Q

Isoleucine, Ile, I

A

Nonpolar, nonaromatic side chain

4 carbon alkyl side chain

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10
Q

Methionine, Met, M

A

Nonpolar, nonaromatic side chain
1 of 2 amino acids with a sulfur in its side chain
Sulfur has a methyl group attached

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11
Q

Proline, Pro, P

A

Nonpolar, nonaromatic side chain

Amino nitrogen becomes part of the side chain and creates a 5 membered ring

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12
Q

Tryptophan, Trp, W

A

Uncharged aromatic side chain

Double-ring system that contains a nitrogen

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13
Q

Phenylalanine, Phe, F

A

Uncharged aromatic side chain
Benzyl side chain (benzene + CH2)
Relatively nonpolar

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14
Q

Tyrosine, Tyr, Y

A

Uncharged aromatic side chain
Phenylalanine with an added Oh group on the benzene ring
Relatively polar

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15
Q

Serine, Ser, S

A

Polar, nonaromatic side chain
CH2 + OH side chain
Able to participate in hydrogen bonding

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16
Q

Threonine, Thr, T

A

Polar, nonaromatic side chain
CH3 + C + OH side chain
Able to participate in hydrogen bonding

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17
Q

Asparagine, Asn, N

A

Polar, nonaromatic side chain

CH2 + amide side chain

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18
Q

Glutamine, Gln, Q

A

Polar, nonaromatic side chain

CH2 + CH2 + amide side chain

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19
Q

Cysteine, Cys, C

A

Polar, nonaromatic side chain
CH2 + thiol side chain
Sulfur in side chain is prone to oxidation

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20
Q

Aspartic acid, Asp, D

A

Negatively charged (acidic) side chain
CH2 + carboxylate side chain
Anion is aspartate

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21
Q

Glutamic acid, Glu, E

A

Negatively charged (acidic) side chain
CH2 + CH2 + carboxylate side chain
Anion is glutamate

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22
Q

Lysine, Lys, K

A 
Positively charged (basic) side chain
Terminal primary amino group
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23
Q

Arginine, Arg, R

A 
Positively charged (basic) side chain
3 nitrogens in its side chain
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24
Q

Histidine, His, H

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A 
Positively charged (basic) side chain
Aromatic ring with 2 nitrogen atoms in its side chain (imidazole)
25
Amphoteric species
A species that can either accept or donate a proton depending on the pH of their environment
26
Isoelectric point (pI)
The pH at which the molecule is electrically neutral (zwitterion)
27
pI for neutral amino acids
Calculated by averaging the pKa values for the amino and carboxyl groups (pKa,NH3 group + pKa,COOH group)/ 2
28
pI for acidic amino acids
Calculated by averaging the pKa values for the R and carboxyl groups (pKa,R group + pKa,COOH group)/ 2
29
pI for basic amino acids
Calculated by averaging the pKa values for the amino and R groups (pKa,NH3+ group + pKa,R group)/ 2
30
Peptides
Composed of amino acid residues
31
Dipeptides
Consist of 2 amino acid residues
32
Tripeptides
Consist of 3 amino acid residues
33
Oligopeptides
Relatively small peptides | Up to about 20 amino acid residues
34
Polypeptides
Longer chain of amino acid residues
35
Peptide bonds
The bond that joins the residues in peptides Specialized form of an amide bond that forms between the COO- group of one amino acid and the NH3+ group of another amino acid Example of condensation/dehydration reaction
36
Condensation/dehydration reaction
Results in the removal of a water molecule
37
Proteins
Polypeptides that range from just a few amino acids in length up to thousands
38
Primary protein structure
Linear arrangement of amino acids coded in an organism’s DNA | Stabilized by the covalent bonds between adjacent amino acids
39
Sequencing
Laboratory technique used to determine the primary structure of a protein
40
Secondary protein structure
The local structure of neighboring amino acids | Result of hydrogen bonds between nearby amino acids a-helices and B-pleated sheets
41
a-helices
Rodlike structure in which the peptide chain coils clockwise around a central axis Stabilized by intramolecular hydrogen bonds
42
Keratin
Fibrous structural protein found in human hair, skin, and fingernails a-helix is an important component in the structure
43
B-pleated sheets
Peptide chains lie alongside one another forming rows or strands Stabilized by intramolecular hydrogen bonds
44
Fibrous proteins
Structure resembles sheets or long strands | Collagen
45
Globular proteins
Structure is spherical | Myoglobin
46
Tertiary protein structure
3D shape Determined by hydrophilic and hydrophobic interactions between R groups of amino acids Van der Waals forces, hydrogen bonds, ionic bonds, and covalent bonds
47
Disulfide bonds
Present in tertiary protein structure Form when two cysteine molecules between oxidized to form cystine Create loops in the protein chain
48
Molten globules
Intermediate state in between the secondary structure and the tertiary structure
49
Denaturation
When the 3D structure of protein is changed, causing the protein to no longer function
50
Solvation layer
Formed by nearby solvent molecules when a solute dissolved in a solvent
51
Quaternary protein structure
Only exist for proteins that contain more than one polypeptide chain An aggregate of smaller globular peptides and represents the functional form of the protein Van der Waals forces, hydrogen bonds, ionic bonds, and covalent bonds
52
Cooperativity/allosteric effects
One subunit can undergo conformational or structural changes, which can either enhance or reduce the activity of the other subunits
53
Conjugated proteins
Proteins with covalently attached molecules called prosthetic groups
54
Prosthetic groups
Small molecules permanently attached to the enzyme Can be organic molecules (vitamins) or metal ions (iron) Direct proteins to be delivered to certain locations
55
Lipoproteins
Proteins with lipid prosthetic groups
56
Glycoproteins
Proteins with carbohydrate prosthetic groups
57
Nucleoproteins
Proteins with nucleic acid prosthetic groups
58
Heme
Iron-based, pigment part of hemoglobin

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