Lecture 3 Flashcards by Mia McCombs

What are the amino acids?

basic building block of proteins

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How many amino acids are there?

20 that make up all proteins

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What is the R group bound to?

a-carbon

aka side chain

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What is the Nitrogen tail of an amino acid?

the amino group

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What is the COH end of an amino acid?

the carboxyl group

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What are the classes of amino acids?

aliphatic
aromatic
sulfur containing
alcohols
bases
acids
amides

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What are the four aliphatic amino acids?

alanine (A)
valine (V)
leucine (L)
isoleucine (I)

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What are the two aliphatic/structural amino acids?

proline (P)
glycine (G)

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What are the two aromatic amino acids?

tryptophan (W)
phenylalanine (F)

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What is the aliphatic/sulfur-containing amino acids?

methionine (M)

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What are the two carboxylic acid amino acids and what are their pKa’s?

aspartic acid (D) 4.1
glutamic acid (E) 4.1

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What is the aromatic amino acid and what is its pKa?

tyrosine (Y) 10.9

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What is the thiol/structural amino acid and what is its pKa?

cysteine (C) 8.3

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What is the amine amino acid and what is its pKa?

lysine (K) 10.8

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What is the guanidinium amino acid and what is its pKa?

arginine (R) 12.5

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What is the imidazole amino acid and what is its pKa?

histidine (H) 6.0

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What are the two alcohol amino acids?

serine (S)
threonine (T)

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What are the two amide amino acids?

asparagine (N)
glutamine (Q)

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What are the two transamination amino acids?

aspartic acid (D)
asparagine (N)

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What are the hydrophobic amino acids?

A (alanine)
V (valine)
L (leucine)
I (isoleucine)
M (methionine)
W (tryptophan)
F (phenylalanine)
G (glycine)
P (proline)

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What are the acidic amino acids?

E (glutamic acid)
D (aspartic acid)
C (cysteine)
Y (tyrosine)

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What are the basic amino acids?

K (lysine)
R (arginine)
H (histidine)

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What are the polar amino acids?

S (serine)
T (threonine)
N (asparagine)
Q (glutamine)
D (aspartic acid)

What can form disulfide bonds?

Cysteine (CYS) (C)

What does C, CYS, Cysteine do?

plays important functional and structural roles

What is C, CYS, Cysteine important for in regards to function and structure?

-the catalytic function of many enzymes (the deprotonated -SH group is a good nucleophile) -it can form disulfide bonds SH groups must be close in space

What is oxidation?

loss of e-

What is reduction?

gain of e-

What are reducing conditions in the cell due to?

due to Glutathione (GSH) GSH is a tri-peptide (ECG) with a reducing thiol

What can P,PRO, Proline do?

can assume both cis and trans conformations

In proteins, are peptide bonds generally cis or trans? And what is the exception?

trans proline if it is the aa following the bond

What are the four properties of amino acids?

1) amino acids are chiral 2) amino acids prefer diff. solvent environments (hydropathy) 3) amino acids are charged 4) amino acids can be Ionized

Natural amino acids have what configuration? And what is its enantiomer/mirror image?

L, alanine D and L are enantiomers

What is hydropathy?

the relative hydrophobicity of each amino acid (measure of polarity)

The amino group and/or carboxyl group will be charged depending on the what?

depending on the pH

Can the R group be charged?

yes it could

At neutral pH amino acids are predominantly what?

dipolar ions (zwitterions)

How many chiral centers and stereoisomers does Isoleucine (ILE) have?

2 chiral centers 4 possible stereoisomers

What does amino acid ionization state depend on?

depends on pH

What are the ionizable groups in amino acids?

1) carboxyl group 2) amino group 3) some side chains

What does each ionizable group have?

has a specific pKa

For a solution pH BELOW the pKa, the _____ form (__) predominates. For a solution pH ABOVE the pKa, the _____ (conjugate base) form (__) predominates?

For a solution pH BELOW the pKa, the PROTONATED form (AH) predominates. For a solution pH ABOVE the pKa, the UNPROTONATED (conjugate base) form (A-) predominates?

When is pKa the pH?

when concentrations of [AH] and [A-] are equal

All amino acids have how many charged groups?

at least 2 charged groups

What is the pKa of Cysteine?

8.4

What is the pKa of Tyrosine?

10.5

What is the pKa of Asparagine?

10.5

What is the pKa of Glutamine?

10.5

What is the pKa of Aspartic acid?

3.9

What is the pKa of Glutamic acid?

4.1

What is the pKa of Lysine?

10.5

What is the pKa of Arginine?

12.5

What is the pKa of Histidine?

6.0

The ratio of unprotonated to protonated R-group changes by an order of magnitude with each what?

with each change in pH unit relative to the groups pKa

Titration curves are used to determine what?

pKa values

In a titration curve, what is pI (isoelectric point)?

the pH where the net charge is 0 (so in the middle between pK1 and pK 2) 2.4+9.9 / 2 = 6.15

What is the net charge of the left side and then the right side? What is the pI of the two?

Left side: Net charge +1 Right side: Net charge 0 explanation=, look at all the + and - and cancel them out then see results pI = 7.65 (6.0 +9.3)/2