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BMS > Amino Acids > Flashcards

Amino Acids Flashcards

1
Q
A

Glycine (G, gly)

Nonpolar

properties: achiral, good if you need a small side chain tends to destabilize proteins, flexible.

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2
Q
A

Alanine (A, ala)

Nonpolar

properties: tetris AA (packs nicely in interior of proteins)

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3
Q
A

Leucine (L, leu)

Nonpolar

properties: tetris AA (packs nicely in interior of proteins)

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4
Q
A

Isoleucine (I, ile)

Nonpolar

properties: tetris AA (packs nicely in interior of proteins)

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5
Q
A

Methionine (M, met)

Nonpolar

properties: tetris AA (packs nicely in interior of proteins), S is inert

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6
Q
A

Tryptophan (W, trp)

Nonpolar

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7
Q
A

Phenylalanine (F, phe)

Nonpolar

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8
Q
A

Proline (P, pro)

Nonpolar

properties: imino acid, 15% in cis, stabilizing effect on protein

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9
Q
A

Serine (S, ser)

Uncharged polar

properties: Hydrogen binding, can be phosphorylated, O-linked glycosylation

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10
Q
A

Threonine (T, thr)

Uncharged polar

properties: can be phosphorylated, H bonding, )-linked glycosylation

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11
Q
A

Tyrosine (Y, tyr)

Uncharged polar

properties: H bonding, phosphorylation

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12
Q
A

Asparagine (N, asn)

Uncharged polar

properties: amide, good for H bonding, N-linking glycosylation

*(think N for everything!)*

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13
Q
A

Glutamine (Q, gln)

Uncharged polar

properties: good N donor, high concentraion in cells for N donating

*too long for other properties*

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14
Q
A

Cysteine (Y, cys)

Uncharged polar

properties: sulfhydryl, able to form cross-links via disulfide bonds

disulfide bonds- only occurs in oxidizing environments (typically outside cells) or lysosomes, stabilize the structure, requires specific orientations and distances, can be intrachain or interchain

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15
Q
A

Glutamic acid (E, glu)

Acidic

pKa: 4

properties: N donor

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16
Q
A

Aspartic Acid (D, asp)

Acidic

pKa: 4

properties: H bonds, catalyzes reactions, nucleophile

17
Q
A

Histidine (H, his)

Basic

pKa: 6

properties: imidazole

18
Q
A

Lysine (K, lys)

Basic

pKa: 10

properties: guanidinium, planar, good H bonding

19
Q

Properties of Amino Acids

A

Free AA exists in this form

stereochem: L-Configuration in proteins (“CORN” looking from H down to C)

pKa amino group: 9

pKa carboxyl group: 2

20
Q

Properties of the Peptide Bond

A

N terminus –> C terminus

2 amino acids comes together, lose a water, and form a C-N bond

The two alpha carbons form a planar backbone

peptide bond is polar (neutralize polarity via H bonds on the insideof proteins)

sp2 hybrid orbitals (π bond)

21
Q

Configurations of Peptide Bonds

A

mostly in trans (except for 15% prolines in cis)

backbone in a plane with C alphas in the corners

angles to allow planes to rotate relative to eachother:

  • Φ: C alpha (@ point in both planes) to N
  • Ψ C alpha (@ point in both planes) to C’
22
Q

Primary Structure

A

amino acid sequence, defined by covalent bonds including disulfide bridges (between cysteine)

23
Q

Secondary Structure

A

Local arrangements of the peptide backbone, often defined by H-bonds

if repeated phi psi angles:

Alpha helix & beta sheet

if non repeating phi psi angles:

loops & turns

24
Q

Tertiary Structure

A

Arrangement of secondary structure elements into compact domain…i.e. a globular unit

25
Q

Quaternary Structure

A

arrangement of multiple polypeptide chains in a multisubunit protein (oligomers like hemoglobin)

26
Q

Alpha Helix

H bonding, polarity, and dimensions

A

right handed

C=O points to C terminus (dipole)

residues separated by 3 positions for H bonds between backbone atoms

* (bonds are formed bw C=O of residue I to H of residue i+4)

dimensions: 3.6 residues/turn, 5.4 A/turn, 1.5 A rise/ residue

27
Q

Classification of Helices

A

can be hyrophobic (buried) or polar (exposed) but most are amphipathic…meaning half polar half hydrophobic

when this protein packs, the nonpolar residues will be buried on the inside and the polar residues will be exposed on the surface of the protein

28
Q

Beta Sheets

directions and dimensions

A

come together via H bonding in parallel or antiparallel strands to form sheets

directions:

strands in one plane with side chains above and below the sheet

dimensions: 3.5 A / residue

29
Q

Beta sheets

characteristics of parallel sheets

A

hydrophobic residues above and below plane.. so typically buried

wrapping with amphipathic helices from the N terminus to the C terminus called “Beta bends”

30
Q

Beta sheets

characteristics of anti-parallel sheets

A

amphipathic (hydrophobic residues above, hydrophilic residues below), so exposed ons urface of proteins

easy to connect N with C (sm amino acid chane, dont have to cross over the plain like in parallel sheets)

31
Q

Turns and Loops

characteristics

A

non-repetitive secondary structure

make up 50% of proteins

FUNCTIONAL residues:

occur on surfaces of proteins (exposed to solvents/binding sites)

32
Q

Motifs

(supersecondary structures)

A

A: helix-loop-helix

B: B-hairpin

C: Greek Key

D: B-a-B

33
Q

Average molecular weight of an amino acid residue

A

110 Da

34
Q

Fibrous proteins

A

structural proteins

elongated and LARGE in mass

ex) used in tissue formation (collagen, elastin)

35
Q

Globular proteins

A

dynamin functions

spherical

examples) used in transport, immune system, metabolism, catalysis (enzymes), gene expression, muscle contraction

36
Q

Forces that stabilize proteins

A

Hyrdrophobic: side chains pack to form core

Van der Waals: weak but numerous

Hydrogen bonds: stabilize and neutralize backbone

Ionic interactions: charged residues (amino + carbox)

Disulfide bridges: cysteine covalently binds two chains together

37
Q
A

primarily alpha proteins

can be parallel or perpendicular

38
Q
A

primarily B proteins

form a barrel to bury hyrdophobic residues

top: anti-parallel and contiguous
bottom: anti-parallel and two greek keys that join at a face

39
Q
A

alpha/beta proteins (most common for proteins)

top: alpha helix are all parallel, beta sheets forming a barrel
bottom: domain 2

BMS (3 decks)

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