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Biochemistry > Amino Acids, Peptides, Proteins > Flashcards

Amino Acids, Peptides, Proteins Flashcards

1
Q

Amino Acids

A

molecules that contain two functional groups: amino (NH2) and carboxyl (COOH)

also has one Hydrogen and side chain R-Group

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2
Q

Proteinogenic Amino Acids

A

the 20 alpha amino acids

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3
Q

Alpha-Carbon

A

4 different groups attached to it so its chiral

most amino acids are optically active/chiral except Glycine (2 Hs)

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4
Q

All chiral amino acids in Eukaryotes are ______. This is an ____ absolute configuration.

This does not apply to ____ as it is ________ amino acid but as _______ configuration

A

L-amino acids

S

cysteine

L

R

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5
Q

Non-Polar, Non Aromatic Side Chains

A 
glycine
alanine
valine
leucine
isoleucine
methionine
proline
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6
Q

Aromatic Side Chains

A

uncharged aromatic side chains

Tryptophan
Phenyalanine
Tyrosine (phen with OH)

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7
Q

Polar Side Chains

A

Serine and THreionine (OH)

Aspargine and Glutamine (Coo- with NH2 terminal)

Cysteine (thiol)

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8
Q

Negatively Charged (Acidic) Side Chains

A

aspartate/aspartic acid

glutamate/glutamic acid

end with a carboxyl group (acid has a full carboxyl, the anion hs the charge)

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9
Q

Positively Charged (Basic) Side Chains

A

Arginine (3 N groups)
Lysine (ends with NH2)
Histidine (aromatic pentane with an NH with addable H)

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10
Q

Amino acids with long alkyl chains are strongly ______ and found in the ___ parts of protein

All chains with charged side chains are ______.

A

hydrophobic

interior

hydrophillic

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11
Q

Amino Acid Abbreviations: Alanine

A

Ala, A

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12
Q

Amino Acid Abbreviations: Arginine

A

Arg, R

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13
Q

Amino Acid Abbreviations: Asparagine

A

Asn, N

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14
Q

Amino Acid Abbreviations: Aspartic Acid

A

Asp, D

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15
Q

Amino Acid Abbreviations: Cysteine

A

Cys, C

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16
Q

Amino Acid Abbreviations: Glutamic Acid

A

Glu, E

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17
Q

Amino Acid Abbreviations: Glutamine

A

Gln, Q

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18
Q

Amino Acid Abbreviations: Glycine

A

Gly, G

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19
Q

Amino Acid Abbreviations: Histidine

A

His, H

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20
Q

Amino Acid Abbreviations: Isoleucine

A

Ile, I

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21
Q

Amino Acid Abbreviations: Leucine

A

Leu, L

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22
Q

Amino Acid Abbreviations: Lysine

A

Lys, K

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23
Q

Amino Acid Abbreviations: Methionine

A

Met, M

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24
Q

Amino Acid Abbreviations: Phenylaline

A

Phe, F

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25
Amino Acid Abbreviations: Proline
Pro, P
26
Amino Acid Abbreviations: Serine
Ser, S
27
Amino Acid Abbreviations: Threonine
Thr, T
28
Amino Acid Abbreviations: Tryptophan
Trp, W
29
Amino Acid Abbreviations: Tyrosine
Tyr, Y
30
Amino Acid Abbreviations: Valine
Val, V
31
Amphoteric Apecies
able to accept a proton or donate a proton depending on the pH of the environment
32
Ionizable groups tend to ___ protons under acidic conditions and ____ them under basic conditions.
gain | lose
33
If pH < pKA, a species will be ______ If pH > pkA species will be ____
protonated deprotonated
34
Zwitterions
multicharged, dipolar ions whose charges cancel out
35
When pKas are met, the amount of _____ and protonated/deprotonated amino acid are the same. The titration curve is ____and the solution is acting as a _____
zwitterion flat buffer
36
Isoelectric Point
every molecule is a neutral zwutteruib. pH- pImeans neutral solution pI = pKaNH3 + pKaCOOH / 2
37
When molecule is neutral, it is very sensitve to ______, hence titration curve is _____
pH change vertical
38
pI For Acidic Amino Group (fully protonated charge +1)
pI = pKa R + pKaCOOH /2 so its low
39
pI For Basic Amino Group (fully protonated state charge +2)
pI = pKa R + pKaNH /2 so its high
40
Peptides
consist of amino acid subunits/residues
41
Oligo vs Polypeptides
small peptides upto 20 residues longer chains of residues
42
Peptide Bonds
join peptide bonds together between the COO- and NH3+ of 2 amino acids formed via dehydration/condensation partial double bond characteristic due to carbonyl and lone pair on amino nitrogen, thus resonance occurs
43
Condensation Reaction of Peptide Bonds
electrophillic carbonyl carbon is attacked by nucleophillic amino group of another amino acid and hydroxyl of carboxy is kicked off
44
No rotation aroun the ______ bond
Carboxy-Amino
45
Hydrolysis of proteins is carried out by _____ or ______. They cleave at ______ of the peptide chain by adding a ______ to the _____ and a _____ to the _______.
trypsin chymotrypsin specific parts H amino OH carbonyl
46
Proteins
polypeptides that range from a few amino acids to thousands and act as: enzymes, hormones, membrane pores and receptors
47
Primary Structure
linear sequence from N amino end to C carboxy end stabilized by: covalent peptide bonds allows for encoding for high folding structures can be sequenced
48
Secondary Structure Alpha Sheets
hydrogen bonding between amino acids coils around a central axis intramolecular hydrogen bonds between carbonyl oxygen and adjacent amino hydrogen, side chains point away from coil
49
Secondary Structure Beta Sheets
parallel or antiparallel peptide chains lie alongside one another by intramolecular hydrogen bonds between carbonyl oxygen and amide hydrogen in adjacent chain rippled/pleated to accomodate for most H bonds R groups are above or below the plane of the sheet
50
Due to itsrigid, cyclic nature, ____ will cause kinks in peptide chains in a ______ structure, hence theya re rarely found in them. They are rarely found in middle of _____ but are in the ___ between chains of B pleated sheets and at the start of a alpha helix.
proline alpha helix pleated sheets turns
51
Tertiary Structure
determined by hydorphobic and hydorphillic interactions between R groups of amino acids stabilized further by electrostatic and hydrogen bonds between hydrophillic residues that get pulled within. Also have disulfide bonds from two cysteine molecules oxidizing to make structure more stable amino acids have charged/polar R groups on the outside
52
Molten Globules
intermediate states between secondary structure, hydrophobic interactions/H bonding and three dimensional shape
53
Denaturation
protein losing its tertiary structure, thereby losing its function
54
Solvation layer
when solute dissolves in a solvnt, the solvent molecules form a layer around the solute when hydrophobic residues in contact with water, difficulty in making h-bonds so water rearranges itself (cages) to create a negative change in entropy making it unfavorable (delta G gets more positive so nonspontaneous) opposite occurs for hydrophillic residues
55
Quaternary Structure
not all proteins have Quaternary structure aggregate of smaller globular peptides/subunits that represent function Pros - more stable by reducing SA of protein complex - reduce DNA needed to code complex - Bring catalytic sites together - Induces Cooperativity/allosteric effects
56
Hemoglobin
4 distinct subunits which can each bind to one oxygen, so it can carry a total of 4
57
Conjugated Proteins
derive function from covalently attached molecules known as prosthetic groups
58
Prosthetic Groups
can be organic molecules or metals lipoproteins (lipid) glycogrpoteins (carbohydrate) nucleoproteins (nucleic acid)
59
Two main causes of denaturation are
temperature and solutes
60
When temperature gets to high, it can overcome the _____ which hold the proteion together and cause it to unfold.
hydrophobic interactions
61
Solutes can denature proteins by breaking ______, overcoming ______ and other side chain interactions and non-covalent bonds.
disulfide bonds (cysteine goes to 2 cysteines) hydrogen bonds

Biochemistry (5 decks)

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