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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
Q

Amino Acid Abbreviations: Proline

A

Pro, P

26
Q

Amino Acid Abbreviations: Serine

A

Ser, S

27
Q

Amino Acid Abbreviations: Threonine

A

Thr, T

28
Q

Amino Acid Abbreviations: Tryptophan

A

Trp, W

29
Q

Amino Acid Abbreviations: Tyrosine

A

Tyr, Y

30
Q

Amino Acid Abbreviations: Valine

A

Val, V

31
Q

Amphoteric Apecies

A

able to accept a proton or donate a proton depending on the pH of the environment

32
Q

Ionizable groups tend to ___ protons under acidic conditions and ____ them under basic conditions.

A

gain

lose

33
Q

If pH < pKA, a species will be ______

If pH > pkA species will be ____

A

protonated

deprotonated

34
Q

Zwitterions

A

multicharged, dipolar ions whose charges cancel out

35
Q

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 _____

A

zwitterion

flat

buffer

36
Q

Isoelectric Point

A

every molecule is a neutral zwutteruib. pH- pImeans neutral solution

pI = pKaNH3 + pKaCOOH / 2

37
Q

When molecule is neutral, it is very sensitve to ______, hence titration curve is _____

A

pH change

vertical

38
Q

pI For Acidic Amino Group (fully protonated charge +1)

A

pI = pKa R + pKaCOOH /2

so its low

39
Q

pI For Basic Amino Group (fully protonated state charge +2)

A

pI = pKa R + pKaNH /2

so its high

40
Q

Peptides

A

consist of amino acid subunits/residues

41
Q

Oligo vs Polypeptides

A

small peptides upto 20 residues

longer chains of residues

42
Q

Peptide Bonds

A

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
Q

Condensation Reaction of Peptide Bonds

A

electrophillic carbonyl carbon is attacked by nucleophillic amino group of another amino acid and hydroxyl of carboxy is kicked off

44
Q

No rotation aroun the ______ bond

A

Carboxy-Amino

45
Q

Hydrolysis of proteins is carried out by _____ or ______. They cleave at ______ of the peptide chain by adding a ______ to the _____ and a _____ to the _______.

A

trypsin

chymotrypsin

specific parts

H

amino

OH

carbonyl

46
Q

Proteins

A

polypeptides that range from a few amino acids to thousands and act as:

enzymes, hormones, membrane pores and receptors

47
Q

Primary Structure

A

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
Q

Secondary Structure Alpha Sheets

A

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
Q

Secondary Structure Beta Sheets

A

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
Q

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.

A

proline

alpha helix

pleated sheets

turns

51
Q

Tertiary Structure

A

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
Q

Molten Globules

A

intermediate states between secondary structure, hydrophobic interactions/H bonding and three dimensional shape

53
Q

Denaturation

A

protein losing its tertiary structure, thereby losing its function

54
Q

Solvation layer

A

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
Q

Quaternary Structure

A

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
Q

Hemoglobin

A

4 distinct subunits which can each bind to one oxygen, so it can carry a total of 4

57
Q

Conjugated Proteins

A

derive function from covalently attached molecules known as prosthetic groups

58
Q

Prosthetic Groups

A

can be organic molecules or metals

lipoproteins (lipid)
glycogrpoteins (carbohydrate)
nucleoproteins (nucleic acid)

59
Q

Two main causes of denaturation are

A

temperature and solutes

60
Q

When temperature gets to high, it can overcome the _____ which hold the proteion together and cause it to unfold.

A

hydrophobic interactions

61
Q

Solutes can denature proteins by breaking ______, overcoming ______ and other side chain interactions and non-covalent bonds.

A

disulfide bonds (cysteine goes to 2 cysteines)

hydrogen bonds

Biochemistry (5 decks)

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