1
Q
define pKa
A
- pKa tells you what the pH needs to be in order for a chemical species to donate or accept a proton.
- if a pH is higher than a compounds pKa then that compound will donate a H!
2
Q
define pI
A
- the isoelectric point
- is the pH at which a particular molecule carries no net electrical charge in the statistical mean.
3
Q
what is the predominant form of amino acids in biology
A
L-alpha-amino acids
4
Q
name the non-polar aliphatic R-group amino acids
A
- glycine
- alanine
- valine
- leucine
- isoleucine
- proline
- methionine
5
Q
name the polar, uncharged R-groups
A
- serine
- threonine
- cysteine
- asparagine
- glutamine
6
Q
positively charged R-groups
A
- Lysine
- arginine
- histidine
7
Q
aromatic R groups
A
- Phenylalanine
- Tyrosine
- Tryptophan
8
Q
Negatively charged R-Groups
A
Aspartate
-Glutamate
9
Q
In what organisms is proline commonly found
A
-thermophilic organisms
10
Q
What mutation occurs in sickle cell anemia ??
A
Glutamic Acid to Valine (E6V)
11
Q
Maple Syrup Urine Disease
A
- branched-chain ketoaciduria
- Mneumonic “LIV Maple Syrup”
- Mutations in any of these three genes reduce or eliminate the function of the protein complex, preventing the normal breakdown of leucine, isoleucine, and valine. As a result, these amino acids and their byproducts build up in the body. Because high levels of these substances are toxic to the brain and other organs, their accumulation leads to the serious health problems associated with maple syrup urine disease.
12
Q
Tryptophan is a precursor to
A
- Trp (W)
- precursor to serotonin
13
Q
Tyrosine is a precursor to
A
- Tyr (Y)
- precursor to chatecholamines
14
Q
Phenylketonuria (PKU)
A
-defect in catabolism of phenylalanine
-can be extremely painful if untreated with careful diet
-Developmental: delayed development, failure to thrive, short stature, or slow growth
Cognitive: intellectual disability or slowness in activity
Also common: atopic dermatitis, body odor, loss of skin color, seizures, or urine odor
15
Q
Aromatic side chains absorb
A
- UV light
- W>Y»F
16
Q
Lambert Beer Law
A
- log (Io/I)= A= epsilon * c * d
- this allows biochemists to measure the concentration of protein
17
Q
give the pKa of Y’s R-group
A
- Tyrosine=Tyr=Y
- pKa 10.07
18
Q
give pKa of C’s R-group
A
- Cysteine=Cys=C
- pKa = 8.18
19
Q
give pKa of K’s R-group
A
-Lysine=Lys= K
=10.53
20
Q
give pKa of H R-group
A
Histidine=His=H
-6.00
21
Q
give pKa of R’s R-Group
A
- Arginine= Arg=R
- 12.48
22
Q
give pKa of D’s R-group
A
- Aspartate= Asp=D
- 3.65
23
Q
give pKa of E’s R-Group
A
Glutamate=Glu=E
-4.25
24
Q
Name the essential amino acids
A
-PVT TIM HLL
Phenylalanine
Valine
Threonine
Tryptophan
Isoleucine
Methionine
Histidine
Leucine
Lysine
25
what 7 AA sidechains are readily ionizable in aqueous solution
- Glutamate
- Aspartate
- Arginine
- Lysine
- Histidine
- Tyrosine
- Cysteine
26
what 10 AA are not ionizable whatsoever
- glycine
- Alanine
- Valine
- Leucine
- Isoleucine
- Asparagine
- Glutamine
- Phenylalanine
- Proline
- Methionine
* Double Check
27
3 amino acidsidde chains not ionizable to any specific extent in water, but can donate protons
-threonine
-Serine
-Tryptophan
Double check
28
describe the sickle cell mutation
E6V
| - Missense mutation from hydrophilic Glu to hydrophobic V
29
which amino acid is a precursor to serotonin?
Trp (W)
30
which amino acid is a precursor to catecholamines
Tyr (Y)
31
which amino acid is a precursor to Tyr (Y)
Phe (F)
32
Histidine can be metabolized to
histamine
33
which AA is best at absorbing UV light?
Trp (W)
34
Beer's Law
[x]/A = [x]/A
ultimately, the darker the solution, the more concentrated it is :)
: log (Io/I)= A= epsilon*concentraion* d (light path distance)
35
two juxtaposed cysteines can be ____ to form a covalent disulfide bond
-oxidized
36
Molecular Weight of Amino Acids calculated by
of n-peptide is sum of n amino acids - mass of (n-1) waters
37
Sanger degradation is really only useful for
determining the first amino acid
38
what is a useful strategy top sequence a protein?
-cleave protein with a few different reagents and then sequence several peptides each by Edman degradation and then identify overlapping sequences
39
Collagen
- important protein in connective tissue including: tendons, ligaments, bone, and skin
- 3 chains intertwined as a left-handed triple helix
40
D-amino acids
- long lived in bodies
| - have the same chemistry as normal 'R' groups
41
properties of the peptide bond
- its a product of condensation rxn between the -COO- and NH3+ from 2 amino acids
- involves 6 atoms (from C alpha1-Calpha2)
- the C-O and C-N bonds fall between the single and double bond lengths
- nearly planar; partial double bond character
42
cis or trans when Ω =0
cis
43
cis or trans when Ω =180
trans
44
Calpha-C-N-Calpha refers to
peptide bond or Ω omega torsion angle
45
C-N-Calpha-C refers to
Φ
46
N-Calpha-C-N refers to
Ψ
47
What is the approximately length of a peptide bond in Angstroms?
1.32 A
48
How many residues constitute five complete turns of a regular alpha helix?
18
49
how many residues in one turn of an alpha helix?
3.6
50
```
Identify the strongest interaction:
Disulfide bridges
Hydrogen bonds
Hydrophobic interactions
Charge-charge interactions
Van der Waals interactions
```
Disulfide bonds
51
describe the properties of the turn of an alpha helix
- 3.6 residues/turn
| - 5.4 Ang
52
the backbone atoms in a-helix core are tightly packed to
- maximize van der Waals contacts
| - exclude free water
53
5 constraints affect alpha-helix stability
1. electrostatic attraction or repulsion involving adjacent AAs with charged R groups
2. bulkiness of adjacent R groups
3. interactions between R-groups (3-4 residues apart)
4. occurrence of Pro or Gly in sequence
5. interactions between charges of AA R-groups near ends of an a-helical segment
54
Beta strands align side by side to maximize
main-chain H bonds and form B-sheets
55
B-turns: Type 1
has proline at 2nd position
56
B-turns: Type 2
has glycine at 3rd position
57
Random coil
-nonrepetitive, but ordered secondary structure elements
| -
58
Circular Dichroism
- empirical specroscopic estimation of secondary structure content
- can be used as a real time measure of protein folding
- dual scans of wavelengths into far UV regions and wavelength is plotted against delta E
59
Guiding Principles of Proteins
1. the 3D structure of a protein is determined by amino acid sequence
2. the function of a protein depends on its exact 3D structure
3. the exact 3D structure of each protein is unique in detail
4. the most important stabalizing forces of native conformations are extremely numerous, weak, non-covalent interactions
60
define motiff
- supersecondary structures
- distinct folding patterns consisting of one or more secondary structures elements
- can be a whole protein or a small part of a large protein
61
define domain
-independently folding and sometimes independently functioning parts of a protein
62
motiff versus domain
you often find that a protein contains multiple domains, each domain characterized by having a sequence that matches the motif of its family.
-domains are structurally independent
63
give hierarchy structure of proteins
primary structure--> secondary structure--> motiffs-->domains-->tertiary structure
64
Levinthal's paradox
- protein folding cannot operate via trial and error
| - would take 10^77 years to explore all conformations
65
Arfinsen's RNAase A Refolding
- used urea to disrupt H-bonds
- used B-mercaptoethanol to break disulfide bonds
- high recovery rate provided evidence that AA sequence must have controlled correct refolding of tertiary structure
66
Examples of modification: S, T, Y
phosphorylation
67
Lysine modification
Methylation, Acetylation, Ubiquitylation
68
palmitoylation
-often a thioester linkage on cysteine near protein C-terminus
69
Hb B-E6V
Hemoglobin beta chain Glu at position 6 changed to Val
70
Liquid Chromatography: Anion exchange
- column elute with NaCl
- the bead material is +
- anions are attracted to resins
71
Cation exchange
- column elute with NaCl
| - beads are - charged
72
Gel Filtration
-larger proteins elute earlier than smaller ones
73
Ligand Affinity Chromatography
-best if used as a late step, make sure no chemical modifications will be made to it
74
mass spectrometry
- molecules first ionized in a vacuum
- then introduced into an electric field plus magnetic field
- then molecules follow path through field as function of m/z ratio
75
All standard amino acids incorporated into proteins, except proline, contain
Amino group
76
In an alpha helix, the H- bonding occurs between
Carbonyl oxygen of one peptide bond and the NH group of the 4th amino acid away
77
The most important contribution to the stability of a protein's native conformation appears to be the
Entropy increase from the decrease in ordered water molecules forming a solvent she'll around it
78
When oxygen binds to the heme-containing protein like myoglobin, the two open coordination bonds of Fe2+ are occupied by
One molecule of O2 and one amino acid R-group
79
Experimentation on denaturation and renaturation after the reduction and reoxidation of the S-S bonds in the enzyme ribonuclease have shown that
The primary sequence of RNase is sufficient to determine its specific secondary and tertiary structure
80
Which is more stable form of beta-sheet, parallel or antiparallel
Antiparallel due to linear and stronger H-bonds
81
How does a buffer resist change in pH upon addition of a strong acid
The strong acid reacts with the weak base in the buffer to form a weak acid, which produces few H+ ions in solution and therefore only a small change in pH
82
Size exclusion (gel-filtration) chromatography
Largest molecules elute first because smaller proteins get stuck in beads
83
Blood
- delivers O2, nutrients, antibodies,, signaling molecules, metabolic byproducts, and diverse cells and substances
- large, liquid connective tissue
84
function of Hb
- O2 has very low solubility in blood
| - Hb allows for blood concentrations around 10mM O2(a 100 fold increase)
85
Structure of Mb
-1 polypeptide chain (functions as a monomer)
-1 heme group, 1 per chain binds 1 O2
stored and limits the reactivity of O2
86
Structure of Hb
-4 polypeptide chains (alpha2:beta2)
-4 heme groups, 1 per chain
-binds up to 4 O2
transports and limits reactivity of O2
87
Heme group
-organic group called porphyrin plus 1 Fe2+ metal ion
88
Why isnt heme a good O2 carrier by itself?
-must be part of a large protein to prevent oxidation of the iron atom
89
is heme covalently bound to globin?
no
90
how many coordination bonds does Fe2+ form
6!
| 1 will bond with R group of protein and 1 will bond with O2
91
give the equation for the fractional binding (θ)
θ= [L]/ ([L]+Kd)
92
what does θ tell us?
the fraction of total sites bound by ligand
93
what does Kd tell us?
- Kd gives us the concentration at which 50% of all possible ligand binding sites are actually occupied
- the higher the Kd the lower the affinity
94
The O2 binding to myoglobin curve
-Mb has 1 heme --> 1 O2 binding site
-Mb shows no cooperativity: each O2 binds independently
plot of θ is hyperbolic
95
what polar R-Groups can be readily Phosphorylated?
S, T, and Y
96
Two isomeric aliphatic R groups, one with a second chiral center
I, L
Biochemistry
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