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Biochem > Amino Acids > Flashcards

Amino Acids Flashcards

1
Q

Glucogenic AA

A

Carbon skeleton that is converted to intermediates that can be used to synthesize glucose.

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2
Q

Ketogenic AAs

A

Carbon skeleton is converted to intermediates that can form ketone bodies or fatty acides

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3
Q

What are the essential amino acids

A

TV FILM HWK

-must be obtained from diet

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4
Q

What are the glucogenic nonessential aa’s?

A

DARN CEQ GPS

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5
Q

What are the essential glucogenic

AAs?

A

H MTV

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6
Q

Both nonessential ketogenic and gluconenic AAs

A

Tyrosine

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7
Q

Ketogenic nonessential

A

none

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8
Q

Essenstial both

A

FIW

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9
Q

Essential Ketones

A

LK

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10
Q

What are the characteristics of peptide bonds in AA residues?

A
  • linear and planar
  • not free to rotate; resonance
  • trans: H of amino group is trans to carbonyl group
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11
Q

Bond length of of peptide bond

A

planar bond: 1.32 A

-peptide bond is uncharged

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12
Q

Tans orientation is favored by peptide bond but the exception observed for X-pro is

A

Proline (cis)

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13
Q

What is Phi angle and Psi?

A

Phi: N-C alpha (-80)
Psi: C(alpha)-C (+85)

phi and psi are single bonds

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14
Q

Tertiary Structure

A

folding of polypeptide chain as a result of interactions between R groups.

Ex: helix turn helix

  • helix loop helix
  • zinc fingers
  • leucine zipper
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15
Q

Quaternary Structure

A

interaction of different polypeptide chains to form a functional protein

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16
Q

Secondary structure

A

Hydrogen bonding between carboxyl oxygen and nitrogen hydrogen of the peptide chain (back bone)

  • alpha helix
  • beta sheets
  • beta turns
  • omega loop
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17
Q

How can alpha helix be disrupted?

A

proline

  • large charged amino acids
  • bulky side chains (W)
  • amino acids with branched R groups (V,I)
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18
Q

What stabilizes the hydrogen bonding between alpha helix

A

-carbonyl oxygen
-NH group of peptide
(every fourth AA)

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19
Q

How may AAs per turn of alpha helix and where do r groups extend to?

A
  1. 6 AA per turn

- R groups extend outward

20
Q

What are proteins that contain only alpha helixes?

A

Ferritin, Hemoglobin

21
Q

What do beta bends in beta pleated sheet contain? adjacent aa are seperated by how many angstroms

A

proline and glycine

-3.5 A

22
Q

What are proteins that contain mostly beta sheets?

A

fatty acid binding protein

green flourescent protein

23
Q

Loops and turns connect elements of secondary structure to form domains of

A

omega loops

and beta turn (hairpin)

24
Q

tertiary Folding of polypeptide chain results in interaction between what

A

r-groups

25
Q

Quaternary Structure examples

A

hemoglobin, myoglobin

26
Q

Denaturing protein

A

unfolding and disorganization of proteins secondary and tertiary structure

27
Q

How to denature a protein?

A
  • does not involve hydrolysis of peptide bonds.
  • Denaturing agents: heat, organic solvents, urea, guanidium chloride, detergents (SDS), change in pH, heavy metals

-reducing agents: beta mercaptoethanol

28
Q

Beta mercaptoethanol

A

Reduces disulfide bonds

29
Q

How is Alpha Keratin helizes cross linked?

A
  • Van der Waals forces
  • ionic interactions
  • disulfide bonds

contains heptad repeat; each alpha helix contain 3.5 residues/ turn

30
Q

Collagen describe the structure

A

Composed of long, rigid alpha CHAINS, wrapped around in LEFT handed triple helix

31
Q

Collagen Amino ACid composition

A
  • glycine
  • proline
  • often proline and lysine are hydroxylated
32
Q

What is required in hydrolylation of proline of collagen ?

A
  • prolyl hydroxylase
  • requires vitamin C
  • molecular oxygen

Location: 4 and 3 hydroxyproline

33
Q

Hydroxylation of lysine allows for cross linking. what is the enzyme used

A

lysl hydoxylase

34
Q

Osteogenesis Imperfecta tarda

A

Defects in collagen 1

  • mutation of alpha 1 or alpha 2
  • substitution of AA other than glycine
  • bulky side chain prevents proper folding in alpha chains into helix
35
Q

Osteogenesis Imperfecta congenital

A

type 2 collagen defect

36
Q

What is the purpose of the denaturation and renaturation period?

A

Ribonuclease:
124 AA
4 disulfide bonds
-105 combinations; only 1 combination produces enzymatic activity

37
Q

Differentiate between the two misfolded protein diseases

A

Alzeimers: accumulates in nonbranching fibrils with beta pleated sheet

prion disease (neurons and glial cells): lacks primary sequence differences in postranslational modification.

38
Q

Living systems contain what direction of amino acids

A

L amino acid

39
Q

What does the aromatic AA participate in

A

hydrophobic bonding

  • binding planar ligands via Van der Waals
  • tyrosine may hydrogen bond or donate a catalysis
40
Q

where is serine found in enzymes

A

active site

41
Q

Where are the basic aa found

A

surface and may be found in catalysis or metal binding

42
Q

Ramachandran diagram disfavors phi an psi bonds in

A

beta strands and alpha helixes

43
Q

What does the concentration of disulfide bonds do in hair and wool vs horns, claws

A

More disulfide bonds, make them harder (horns)

hair and wool: less disulfide bonds-more stretchable

44
Q

triple helix structure

A

1000 amino acids
3 amino acids per turn
each alpha chain adapts left handed helix

45
Q

PRotein folding

A

all or none process

-brings amino acid R groups together in active site

Biochem (7 decks)

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