2 Amino acids Flashcards
A-
Non polar
Ala-Alanine- has 3 carbons
G-
Non polar
Gly- glycine- only non chiral AA
V-
Non polar
Val- Valine- branched chain AA
L-
Non polar
Leu-Leucine- branches chain AA
I-
Non polar
Ile- isoleucine- branched chain AA
P-
Non polar
Pro- Proline- only non flexible AA
M-
Met- Methionine- sulfur AA
Amino acids with methyl group as side chain
Alanine
Amino acids forms ring with Nitrogen and side group
Proline
F-
Aromatic
Phe- Phenylalanine
Aromatic AA
Y-
Aromatic
Tyr- tyrosine- has an OH group
W-
Aromatic
Trp- Tryptophan
Largest letter and tryptophan. Is the largest AA
One letter code for phenylalanine
F
S-
Polar uncharged
Ser- Serine- alcohol group
T-
Polar uncharged
Thr- threonine- alcohol group
C-
Polar uncharged
Cys- cysteine- sulfur group
N-
Polar uncharged
Asn- asparagine- amide of Asp
- has amide group so this shows N group
Q-
Polar uncharged
Gln- Glutamine- Amide of Glu
D-
Negatively charged
Asp- Aspartate “asparDick acid”
E-
Negative charged
Glu-glutamate
K-
Positively charges
Lys- Lysine- amine side group
R-
Positively charges
Arg-arginine- guanadino side group
H-
Positively charged
His- Histidine- neutral at pH 7.4, negatively charged only at more acidic pH’s
Most amino acids are composed of:
L- amino acids
What is zwitterion ?
A molecule with equal numbers of positive and negative charges at the same time
What is the side group on G?
-H
Which of the following amino acids is aromatic?
F
Which amino acid is the most abundant in our blood?
Glutamine
What is the one letter code for the aromatic amino acid with the largest molecular weight?
W
Which of the following amino acids has an acidic side group?
E
The amino acid S has an alcohol on it side group
T
What is the one letter abbreviation for tryptophan?
W
C has a side group of
Sulfur
D has a side group of
Acid
F has a side group of
Aromatic
K has a side group of
Basic
Which amino acid has a hydrogen as it site group?
Glycine
At what pH with glycine make a good buffer
2.34
At what pH would there be about a 50 to 50 make sure of glycine with a zero charge and glycine with a -1 charge?
9.60
For the peptide EHWAGLRPG, what is the closest charge at pH 7.4?
0
What is the configuration of the citrulline shown in the attached image
L
At pH of eight, what is the closest charge that would be on histidine?
0
At pH of four, what is the closest charge that would be on histidine?
+1
What pH would there be about a 50:50 ratio of lysine with a positive one charge in the zero charge?
2.34
What is the PI for glycine
5.97
At what pH with glycine make a good buffer?
9.60
DNA has a phosphoric acid backbone, which is why DNA is called deoxyribonucleic acid. At the pH of cells, do you need to be in it’s phosphate state and that’s very negatively charged. DNA is wrapped around histone proteins, which are very positively charged. What amino acids would you expect to be providing those positive charges?
H, K, and R
Glycine has pKa’s of 2.34 and 9.69. At what pH is glycine fully proton acted?
Less than 2.34
Glycine structure
Non polar aliphatic
COO-
l
H3N+-C-H
l
H****
Glycine
Alanine structure
Non polar aliphatic
COO-
l
H3N+-C-H
l
CH3*****
Alanine
Proline structure
Non polar aliphatic
COO-
l
C
/ \.
H2N+ CH2*
l l
*H2C--- CH2*
Proline
Valine structure
Non polar aliphatic
COO-
l
H3N+- C -H
l
CH*
/ \
CH3* CH3*
Valine
Leucine structure
Non polar aliphatic
COO-
l
H3N+-C-H
l
CH2*
l
CH*
/ \
CH3 CH3*
Leucine
Isoleucine structure
Non polar aliphatic
COO-
l
H3N+-C-H
l
H- C- CH3*
l
CH2*
l
CH3*
Isoleucine
Methionine structure
Non polar aliphatic
COO-
l
H3N+-C-H
l
CH2*
l
CH2*
l
S*
l
CH3*
Methionine- sulfur bases and non polar
Phenylalanine structure
Aromatic r groups
COO-
l
H3N+-C-H
l
CH2
l
---------
/ \
\\_\_\_\_\_\_\_\_\_/
Phenylalanine (rings make them more polar)
Tyrosine structure
Aromatic R groups
COO-
l
H3N+-C-H
l
CH2
l
---------
/ \
\\_\_\_\_\_\_\_\_\_/
l
OH
Tyrosinemost polar*
Tryptophan structure
Aromatic R groups
COO-
l
H3N+-C-H
l
CH2
l
C= CH
l \
l NH
l\_\_\_\_/
---------
/ \
\\_\_\_\_\_\_\_\_\_/
TryptophanSerine structure
Polar uncharged R groups
COO-
l
H3N+-C-H
l
CH2OH**
Serine
Threonine structure
Polar, uncharged R group
COO-
l
H3N+-C-H
l
H- C- OH*
l
CH3*
Threonine
Cysteine structure
Polar, uncharged R group
COO-
l
H3N+-C-H
l
CH2
l
SHAsparagine structure
Polar, uncharged r groups
COO-
l
H3N+-C-H
l
CH2
l
C
/ \
H2N O
Asparagine
Glutamine structure
Polar, uncharged R groups
COO-
l
H3N+-C-H
l
CH2
l
CH2
l
C
/ \\
H2N O
Glut amine
Aspartate structure
Negatively charged R groups
COO-
l
H3N+-C-H
l
CH2**
l
COO-**
Aspartate
Glutamate structure
Negatively charged R groups
COO-
l
H3N+-C-H
l
CH2**
l
CH2**
l
COO-**
Glutamate
Lysine structure
Positively charges
COO-
l
H3N-C-H
l
CH2
l
CH2
l
CH2
l
CH2
l
\+NH3
Lysine - Always + charged
Arginine structure
Positively charged
COO-
l
H3N-C-H
l
CH2
l
CH2
l
CH2
l
NH
l
C=+NH2
l
NH2
Arginine - always positive amino acid
Histidine structure
Positively charged
COO-
l
H3N+-C-H
l
CH2
l
C----NH
ll \
ll CH
ll //
C-----N
H
Histidine- sometimes positive when in acidic environment
Which two amino acids are the only two that carry a negative charge at pH 7.4?
Aspartate and glutamate
What is the pH at which one have 10 times more of the acidic or basic form of the drug aspirin?
pKa=3.5
pH=pKa+ log 10( base/ acid)
pH= 3.5 + log10(1/10)
2.5
How many acids are nonpolar?
10 non polar
Glycine, alanine, valine, phenylalanine, tyrosine, tryptophan, methionine, proline, leucine, Isoleucine.
GAVPTTMPLI
How many amino acids are polar?
10 amino acids are polar
Serine, cysteine threonine, lysine, arginine, histidine, asparagine, glutamine, aspartate, glutamate.
SCYLAHAGAG
How do you calculate charges on proteins?
You find the charges of each amino acid in total them up to be the total charge of the protein.
Arginine +1,
Aspartate -1,
glutamate -1,
Lysine has +1
Histidine sometimes +1 at pH less than 6
What happens when 2 Cysteine molecules pair together?
The S amino acid undergoes spontaneous oxidation reaction with oxygen…. Forms a
Disulfide bridge- 2 cysteine a link together
Desmosome
Made up of 4 lysines and creates a central ring
Large cross-link within the protein to make it stronger. These are found in protein elastin which are found in our skin.
Amino acids can act as a buffer within
1 pH unit of its pKa
The pI is the pH at which a titratable molecule has
No charge. This is called the isoelectric point.
The definition of pI is?
The form that has no net charge
At the pK1 the amino acid is:
A 50:50 mixture of protonated vs deportenated carboxylate group
What are the two nonstandard amino acids?
Ornithopter and Citrulline
Which molecular mutation best describes the defect in sickle cell hemoglobin?
Glu➡️Cal at position 6 of the beta chain
Most amino acids will be in what confirmation
Left confirmation
Determine the L and D structures by comparing to:
L and D glyceraldehyde molecule
CHO
l
HO- C- H
l
CH2OH
L- Glyceraldehyde
For the R, just switch the H and OH sides
What is a zwitterion?
It is a molecule that has both positive and negative charges make it ionic but it is also neutral because these charges cancel each other out.
O
ll
-O-- C
l
H3N+--C-H
l
R
ZwitterionSickle cell anemia is when:
The -Glu➡️Val (neutral) on position #6 of the beta chain.
Sickle cell causes fibers to turn into Crystal forms and these cause they sell to sickle out.
The cell becomes less negatively charged which makes it less water soluble because it is also less polar.
Electrophoresis of sickle cell hemoglobin
The normal hemoglobin will move faster towards a positively charged electrode because the negative is attracted to positive. The sickle cell hemoglobin will move slower towards the positively charged electrode because the sickle cell hemoglobin is less negatively charged so it won’t move this quickly.
