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Biochemistry > 2 AA Chem & Prot Organization > Flashcards

2 AA Chem & Prot Organization Flashcards

1
Q

Major structural and fxnal polymers in living systems

A

Proteins

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2
Q

Alphabet of protein structure lol

A

Amino acids

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3
Q

Essential AAs vs Non-Essential AAs vs. Semi-Essential

A

ESSENTIAL:
PVTTIMHALL

*Non-the rest

Semi-essential: some people need it; others don’t i.e. Arg, His

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4
Q

Chirality of amino acids

A

Property of bending light to the left or to the right

If bends to the left = L-config
*natural config in the body

If to the right = D-config

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5
Q

Different classifications of amino acids?

A
  1. Non-polar
    FLAV & I Met & Trp at PGC

A. Aliphatic
GLAVI

  1. Polar
    STYNQ
  2. (+) Charge
    Hug Kiss Run
  3. (-) Charge
    Ef
5. Aromatic
FYT not H
F -benzene
Y - phenyl
W - indole

*Histidine not considered aromatic because its absorption is very weak compared to other amino acids + not aromatic under high pH conditions

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6
Q

Primary sites of linkage of sugars to proteins? Classify.

A

Serine, Threonine, Asparagine (STN)

Polar.

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7
Q

Which of the polar amino acids have a weakly acidic hydroxyl group and may be found on the surface of proteins?

A

Tyrosine.

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8
Q

Which polar AA’s have an amine side chain?

A

N, Q

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9
Q

Why are there (-) charged amino acids?

A

D and E have carboxylic acids in their side chains. These are ionized at pH 7 and thus, carry negative charges on their beta and gamma carboxyl groups.

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10
Q

What is the general acid-base catalyst of many enzymes? What type of ring does it contain?

A

Histidine, imidazole

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11
Q

C

  1. Classification
  2. Importance
  3. Oxidized form
A

Cysteine
1. Non-polar sulfur AA

  1. Important for stabilization of protein structure and formation of a disulfide bond with other cysteine residues
  2. Cystine
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12
Q

Non-polar AA containing a nonpolar methyl thioether group in its side chain

A

Methionine

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13
Q

Cyclic imino acid?

A

Proline

-has a pyrrolidine ring

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14
Q

Glucogenic vs Ketogenic amino acids?

A

Glucogenic - amino acid can be converted to glucose

Ketogenic - amino acid can be converted to ketone bodies

Classification:

G: Rest (*including oxidized C)

K: L K

Both: WIFTY

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15
Q

Amino acids are acidic or basic?

A

Both!! They’re amphoteric.

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16
Q

What is a zwitterion?

A

Compounds with no overall electrical charge but contain separate parts which are + & - charged.

17
Q

pH vs. pKa vs. pI

A

pH - indication if a system is acidic or alkaline

pKa - gives details of dissociation of an acid in aqueous solution

pI - pH at which aa is in its zwitterion form

18
Q

Wild Card:

Draw the structures of the amino acids :)

A

Hehehehe

19
Q

Four levels of protein structure.

A

1’ - aa sequence
2’ - interactions betweens adjacent aa
Tertiary - 3D folding of the polypeptide
Quarternary - arrangements of multiple polypeptides

20
Q

Reaction occurring to form 1’ structure of protein

A

(Between 2 AA forming polypeptide chain): Condensation reaction

21
Q

2’ structure: Alpha-Helix

  • Bonds occurring to stabilize structure
  • Which aa’s favor this structure?
  • Usually right or left-handed?
A
  • H bonds at adjacent regions of helical backbone
  • DELMA
  • Right-handed
22
Q

2’ Structure: Beta sheet

  • stabilized by which bond?
  • Which aa’s more likely to have this form?
A
  • H-bond laterally between peptide band

- IVY

23
Q

Bonds found in a protein
1. Between side chain and carboxyl oxygen

  1. Between two side chains
  2. Between hydrophobic molecules
  3. Between charged particle
  4. Between cysteine amino acids
A
  1. H bond
  2. H bond
  3. Hydrophobic interaction or Van der Waals
  4. Ionic bond
  5. Disulfide bond/bridge
24
Q

Quaternary structure: Peptide structural organization

Bonds:
1. Chemical bond involving sharing of e-

  1. Chemical bond not involving sharing of e-
  2. Involves electrostatic attraction between oppositely charged ions
  3. Between hydrophobic groups
  4. Between side chains or side chain + carboxyl oxygen
A
  1. Covalent Disulfide bonds
  2. Non-covalent Bond
  3. Salt Bridges Ionic Bonding
  4. Hydrophobic interaction
  5. Hydrogen bonds
25
Q

A solution of pure protein is bombarded with radio waves as it is held in a strong magnetic field

A

NMR Spectroscopy

26
Q

Determine 3D surface contours of protein & works well with proteins that form regular pattern in a small crystal or even a membrane

A

Electron microscopy

27
Q

Factors affecting denaturation

A
  1. pH
  2. Temperature
  3. Acid/Base
  4. Pressure
  5. Detergents
28
Q

Chaperones or HSP, disulfide isomerases assist in what process?

A

Protein Folding

29
Q

What if you have abnormalities in:

  1. amyloid beta?
  2. Tau protein?
  3. Alpha-synuclein
  4. Prions
  5. transthyretin
A

Alzheimer’s Disease: 1, 2

Parkinson’s Disease: 1, 2, 3

Mad Cow Disease: 2, 4

Transthyretin Amyloidosis: 5

30
Q

Which part of the amino acid pathway could cause these diseases:

  1. Albinism
  2. Alkaptonuria
  3. Maple Syrup Urine Disease (MSUD)
A
  1. Tyrosinase (Tyrosine -> Melanin conversion)
  2. Urine turns black when exposed to air (Between homogentisic acid —> acetoacetatefumarate)
  3. Branched chain alpha-keto dehydrogenase

Biochemistry (11 decks)

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