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LEG_GSBS Biochem > Smith-AminoAcids > Flashcards

Smith-AminoAcids Flashcards

1
Q

What is the pKa value of carboxylic acid (COOH)?

A

4.4

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2
Q

What is the pKa of an amine (NH+)?

A

6.0

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3
Q

What is the pKa of hydro-sulfur (SH)?

A

8.5

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4
Q

What is the pKa of alcohol (-OH)?

A

10.0

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5
Q

What is the pKa of a -NH3+ group?

A

10.0

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6
Q

What is the pKa of the =NH2+ on arginine?

A

12.0

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7
Q

What is the difference between pKa and pH?

A

pKa is an inherent property of a compound or a functional group which does not change while pH is the measurement of hydronium ions [H+] in solution at a given time.

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8
Q

why is glycine an alpha helix breaker?

A

due to its overt flexibility (lack of stability) and small size

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9
Q

Why is Proline an alpha chain breaker?

A

Due to its steric hinderance. Has no flexibility at all.

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10
Q

What do Ramachandran Plots characterize?

A

The ability of R groups to rotate around their Psi and Phi bonds (angle rotation from -180 to +180

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11
Q

list the organizational forms proteins can make (4) in increasing order

A
  1. secondary structure
  2. motif
  3. domain
  4. quaternary/tertiary structure
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12
Q

define primary structure of protein

A

amino acid sequence

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13
Q

what is secondary structure of proteins

A

angles and structure dictated by the amino acid composition

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14
Q

What is a motif?

A

portion of a protein (e.g. a loop) that is repeated in other proteins

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15
Q

What is a domain?

A

portion of a protein that is physically separate and often has a particular function

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16
Q

What are the major differences between alpha and beta sheets? (two aspects for each)

A

Alpha Helices:
1. bonds within a singluar amino acid sequence
2. all side chains are point outwards
Beta Sheets:
1. separate amino acid sequences in one structure
2. side chains alternate up and down from the plane of the sheet

17
Q

What can govern how a protein folds? (4)

A
  1. Thermodynamics (small proteins)
  2. Kinetics/Translation Order
  3. Helpers (chaperones and refolding proteins)
  4. Heaven Only Knows (huge proteins that end up in rando places)
18
Q

What is PDI?

A

protein disulfide isomerase:
an enzyme found within the endoplasmic reticulum that catalyzes protein folding by forming and breaking disulfide bonds between cysteine residues within proteins as they fold.

19
Q

in what state is PDI active?

A

reduced (has donated electrons)

20
Q

What is peptidylprolyl isomerases?

A

an enzyme found in both eukaryotic and prokaryotic cells that interconverts the cis and trans isomers of proline peptide bonds

21
Q

Most amino acids have a strong energetic preference for the …… peptide bond confirmation due to ….. ……

A

trans
steric hinderance

22
Q

what types of proteins put sugars on proteins?

A

glycosilate proteins

23
Q

Where can glycans (sugars) be linked to your proteins?

A
  1. N-linked glycans
  2. O-linked glycans
  3. Phospho-glycans
24
Q

N-linked glycans are linked to what amino acids typically?

A

asparagine
arginine

25
Q

O-linked glycans are linked to which amino acids typically?

A

serine, threonine, tyrosine, hydroxyproline, hydroxylysine

26
Q

Phospho-glycans are linked to which amino acids typically?

A

phosphoserine

27
Q

N-linked glycosylation requires participation of a special lipid called ….. ……

A

dolichol phosphate

28
Q

For what reasons would we need sugars on proteins?

A
  1. to stabilize the protein
  2. to increase the protein’s solubility
  3. for the protein’s function
  4. -in animals- to monitor the ‘age’ of proteins for degradation
  5. for the protein’s folding process
29
Q

What is the function of glycosilates?

A

to put sugars on proteins

30
Q

What are three important ways proteins can be post-translationally modified?

A
  1. glycosylation
  2. phosphorylation
  3. lipidation
31
Q

What determines the fold of a protein?

A

amino acid composition

32
Q

What determines the function (stability) of a protein?

A

The amino acid composition and fold

33
Q

What is an example of a stable (‘rock’-like) protein?

A

collagen

34
Q
A

LEG_GSBS Biochem (10 decks)

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