Amino Acids Flashcards
1
Q
A
Valine
2
Q
A
Leucine
3
Q
A
Isoleucine
4
Q
A
Methionine
5
Q
A
Phenylalanine
6
Q
A
Asparagine
7
Q
A
Glutamic acid
8
Q
A
Glutamine
9
Q
A
Histidine
10
Q
A
Lysine
11
Q
A
Aspartic acid
12
Q
A
Glycine
13
Q
A
Alanine
14
Q
A
Serine
15
Q
A
Threonine
16
Q
A
Tyrosine
17
Q
A
Tryptophan
18
Q
A
Cysteine
19
Q
A
Proline
59
Q
Polar uncharged amino acids
A
serine
threonine
asparagine
glutamine
cysteine
tyrosine
(STYCNQ)
60
Q
Three letter and one letter abbreviation for:
alanine
A
Ala, A
61
Q
Three letter and one letter abbreviation for:
Arginine
A
Arg/R
62
Q
Three letter and one letter abbreviation for:
Asparagine
A
Asn/N
63
Q
Three letter and one letter abbreviation for:
Aspartic acid
A
Asp/D
64
Three letter and one letter abbreviation for:
Cysteine
Cys/C
65
Three letter and one letter abbreviation for:
Glutamic acid
Glu/E
66
Three letter and one letter abbreviation for:
Glutamine
Gln/Q
67
Three letter and one letter abbreviation for:
Glycine
Gly/G
68
Three letter and one letter abbreviation for:
Histidine
His/H
69
Three letter and one letter abbreviation for:
Isoleucine
Ile/I
70
Three letter and one letter abbreviation for:
Leucine
Leu/L
71
Three letter and one letter abbreviation for:
Lysine
Lys/K
72
Three letter and one letter abbreviation for:
Methionine
Met/M
73
Three letter and one letter abbreviation for:
Phenylalanine
Phe/F
74
Three letter and one letter abbreviation for:
Proline
Pro/P
75
Three letter and one letter abbreviation for:
Serine
Ser/S
76
Three letter and one letter abbreviation for:
Threonine
Thr
T
77
Three letter and one letter abbreviation for:
Tryptophan
Trp/W
78
Three letter and one letter abbreviation for:
Tyrosine
Tyr/Y
79
Three letter and one letter abbreviation for:
Valine
Val/V
80
Which of the following properties of a protein is least likely to be affected by changes in pH?
A) secondary structure
B) primary structure
C) Net charge
D) tertiary structure
primary structure
81
Hydrogen bonding between separate subunits of DNA polymerase is an example of which of the following?
A) 1˚ structure
B) 2˚ structure
C) 3˚ structure
D) 4˚ structure
D) 4˚ structure
82
The unique cyclic structure of what amino acid plays a central role in the **formation of alpha helices and beta sheets**?
proline
83
Electrophoretic separation depends on the existence of...
a negative net charge.
84
Nonpolar, nonaromatic
GAVLIMP
85
Aromatic
FWY
86
Polar
STNCQ
87
Negatively charged
These have COOH in their R groups; DE
88
Positively charged
Amines- RHL
89
Hydrophobic & interior
VAMP-GILF
90
Hydrophilic and protein surface
SYNQC-TWERK-DH
91
Denaturation doesn't affect the …
primary structure
92
and sequence of amino acids from N-terminus (amino acid) → C-terminus (carboxyl end), stabilized by covalent peptide bonds; linear arrangement; (Nterminus = + due to -NH₃⁺
primary structure
93
Local structure of amino acids; from H bonding between a carboxyl oxygen atom and an amide hydrogen atom.
secondary structure
94
side chains point away from helix core; keratin
alpha helices
95
parallel/anti-parallel; peptide chains lie alongside one another; R groups point above & below; fibrogin; proline = kinks
β-pleated sheets
96
3-D shape; stabilized by hydrophobic interactions, acid-base interactions (salt bridges), H bonding, and disulfide bonds.
tertiary structure
97
hydrophobic R groups → protein interior; entropy of surrounding H₂O molecules ↑ = (-) Gibbs
hydrophobic interactions
98
2 cysteine molecules oxidize to create a covalent bond forming cystine. Extracellular space prefers disulfide bond formation (aka an oxidizing environment)
disulfide bonds
99
Interaction b/t peptides in proteins that have multiple subunits; hemoglobin & immunoglobulin. Formation ↓ surface area of the protein complex. Can induce cooperatively (allosteric effects). Assists in conformational stability; brings catalytic cites together; salvation layer
quaternary structure
100
pKa1
carboxyl group
101
pka2
amine group
102
pKa3
side chain
103
For no side chain or a neutral side chain: (pI)=
pI = ½(pKa₁ + pKa₂)
104
For a basic side chain: pI =
pI = ½(pKa₂ + pKa₃)
105
For an acidic side chain: pI =
pI = ½(pKa₁ + pKa₃)
106
Acidic solution; pH =
Acidic solution pH = 1 Has lots of **protons** floating around so anything that can be **protonated** will be
107
Basic solution
pH =
Basic solution
pH=12
Has a lot of **excess hydroxide anions (OH⁻**) so anything that can be **deprotonated** will be
108
Explain isoelectric focusing
In isoelectric focusing, we create a special type of gel and a **pH gradient** along that gel.
We connect both ends of the gel to a **voltage source**, creating an **electric potential difference** between the two sides, creating an **electric field**.
The **proteins** will begin to **migrate** because the proteins will have a net charge and this will interact with the charge of the electric field.
The **anode** has **acidic** gel (**low pH**) and a **(+) charge**. The **cathode** has **basic** gel (**high pH**) and a **(-) charge**.
**Positively charged proteins (pH \< pI)** migrate toward the **(-) cathode** while **negatively charged proteins (pH \> pI)** migrate toward **(+) anode,** and they will continue to migrate until they reach the pH value at which the overall charge is zero (pH = pI).
109
Explain what happens in electrophoresis
The electric field separates the components according to **net charge** and **size**.
• **Positively** charged **anode** at bottom (**oxidation** takes place), **negatively** charged **cathode** at top. (**Reduction** takes place)
**• Small components** and **high charge** move **faster**
* Uses a **polyacrylamide gel,** acts as sieve
* DNA "running to red" = DNA is negatively charged and travels towards the anode
110
Explain what happens in PAGE
Polyacrylamide gel electrophoresis (PAGE)
* 2 variables = **charge & mass**
* Uses sodium dodecyl sulfate (SDS) to page which neutralizes the protein (it's a detergent) taking charge out of the equation, leaving mass as the only variable
* Native Page = retains structure of protein
* SDS-Page = break into subunits
