Block 1 Flashcards
1
Q
Hydroxyl group
A
-OH
2
Q
Amino acids with ring structures
A
phenylalanine, tryptophan, tyrosine
3
Q
Nonpolar amino acids
A
- Surface of membrane proteins
- Hydrophobic, do not form hydrogen bonds
- glycine, alanine, proline, valine, leucine, isoleucine, methionine, tryptophan, phenylalanine
4
Q
Polar amino acids
A
Surface of soluble proteins
-serine, threonine, cysteine, asparagine, glutamine, tyrosine
5
Q
How is the alpha helix stabilized?
A
Hydrogen Bonds
6
Q
What remains intact during protein denaturation?
A
Peptide Bonds
7
Q
Branched Amino Acids
A
Valine, leucine, isoleucine
8
Q
Imino Group
A
Hydrophobic
-Proline
9
Q
Which amino acids can form hydrogen bonds?
A
Serine, Threonine, Tyrosine, Asn, Gln
10
Q
Hydrogen Bonds
A
Non-covalent
11
Q
Disulfide Bonds
A
Covalent
12
Q
Acidic Amino Acids
A
Aspartate and Glutamate (w/o H)
Aspartic acid and Glutamic acid (w/H)
13
Q
Basic Amino Acids
A
Histidine, lysine, arginine
14
Q
Arginine
A
R or Arg
15
Q
Asparagine
A
N or Asn
16
Q
Aspartate
A
D or Asp
17
Q
Glutamate
A
E or Glu
18
Q
Glutamine
A
Q or Gln
19
Q
Phenylalanine
A
F or Phe
20
Q
Tyrosine
A
Y or Tyr
21
Q
Tryptophan
A
W or Trp
22
Q
Lysine
A
K or Lys
23
Q
Strong Acids
A
Completely Dissociates in Water
Very large Ka
-HCl, HBr, HI, HNO3, HClO4, H2SO4
24
Q
Strong Bases
A
Completely Dissociates in Water
Very large Kb
-LiOH, NaOH, KOH, Ba(OH)2, Mg(OH)2
25
Equivalence point
Acid is mixed with equal amounts of Base
26
Buffer
Weak acid and a similar amount of its conjugate base, buffers resist pH change
27
pI
Isoelectric point= no net charge
28
How is acid released from the body?
Exhaled CO2 or excreted in urine
29
Uncharged drugs in the intestinal lumen how?
More readily than charged drugs
30
Primary Protein Structure
Bead on a string, sequence of AA
31
Peptide Bonds
- Formed by a condensation rxn (dehydration)
- Connects 2 AA
- Uncharged and Polar
- Rigid and planar
- no rotation around a peptide bond (double bond)
- prefers trans configuration
- cleaved by Acid hydrolysis
32
Acid Hydrolysis
Cleaves peptide bonds (hydrolyzed by a strong acid at 110C)
33
Chromatography
AA separated by ionic strength and pH
34
Quantified analysis
Ninhydrin, intensity of color measured on spectrophotometer
35
Edman's reagent (phenylisothiocyanate)
Makes N-terminal residue peptide bond weak (cleaves it), only can be used for polypeptides of 100 AA or less
36
Secondary Protein Structure
Alpha Helix, Beta Structure, Beta Bend
| -repetitive hydrogen bonding
37
Alpha Helix
| Secondary Structure
R groups extend outwards
3. 6 residues per turn
- Disrupted by: proline, many charged AA, many AA with bulky side groups, maybe glycine
- helical wheel
38
Beta Sheets
| Secondary Structure
Hydroben bonding, SILK
- parallel: line up in order
- antiparallel: don't line up in order
39
Beta Bend
| Secondary Structure
Usually composed of just a few AA, can link helices and beta sheets to others
40
Supersecondary Structure
Result from folding of secondary structures into small and discrete elements
41
3 Examples of fibrous proteins
1. Silk
2. Keratin
3. Collagen
42
Collagen
Has a triple helix, very tight, most abundant protein in mammals, secondary structure, NOT an alpha helix, fibrous protein, every 3rd AA is glycine
43
Tertiary Structure
When secondary structures fold on themselves, domains
44
```
Globular Proteins
(tertiary structure)
```
Good water solubility
45
Disulfide Bonds
- SH group of 2 cysteines
| - important for insulin
46
Quaternary Structure
More than 1 polypeptide, disulfide bond is not involved
- hemoglobin
- held together by NON-covalent bonds
47
Homomultimer
all same polypeptides
48
Heteromultimer
some polypeptides are different
49
Denaturation
Usually irreversible, loss of biological activity
50
Chaperones
- Keep unfolded proteins separate
- Enhance folding rate
- Synthesis increases with heat
- Reusable
51
Diseases that are resistant to degradation protein?
Alzheimer disease and Prion disease
52
Alzheimer Disease
amyloid-B protein gets degraded causing a possible neurotoxin to be formed and leads to the disease
53
Prion Disease
Scrapie: Sheep
Creutzfeldt-Jakob disease: humans
Mad Cow disease
PrPSc protein
54
Globular proteins
Water soluble, spherical, hydrophobic core
55
Porphyrin Ring
Heme (prosthetic group) after it accepts ferrous ion, can form 6 coordinate covalent bonds
56
Myoglobin
Stores O2 in the cell and delivers to mitochondria when needed, hyperbolic shape
57
Hemoglobin A
4 O2 molecules can be carried, alpha beta peptides, many hydrophobic
58
AA with aromatic side chains
Phenylalanine, Tyrosine, Tryptophan
59
Cooperative ligand binding
Binding of O2 molecule promotes binding of another O2 molecule
60
Positive Allosteric Regulator
Binding of O2 at one site, increases affinity for O2 at another site
61
Enzyme
Biological Catalyst: increase chemical rxn without itself undergoing any permanent chemical change, specific, change the activation energy NOT free energy, use weak non-covalent interactions
62
Substrate
the reactants that are activated by the enzyme
63
Apoenzyme
enzyme without it's nonprotein component
64
Holoenzyme
an active enzyme with its nonprotein component
65
Cofactor
a metallic nonprotein component (Zinc)
66
Coenzyme
non-metallic small organic molecule, typically vitamins
* Co-substrate: transient association (reversible) with the enzyme and dissociates into an altered from (NAD+)
* Prosthetic group: permanent association with an enzyme and the form is not changed at the end of the reaction
67
Turnover number
number of substrate molecules converted to product per enzyme molecule per second
68
Oxidoreductases
Use coenzymes NAD/NADH or FAD/FADH2
| -add an H to the product
69
Transferases
Catalyze transfer of C-, N-, or P-
| -2 substrates, 2 products
70
Hydrolases
Use H2O
71
Lyases
Catalyze cleavage of C-C, C-S, C-N
72
Isomerases
intramolecular rearrangements
73
Ligases
Use ATP to ADP
74
Kinases
adds a phosphate
75
Phosphatase
takes away a phosphate
76
Catalytic Site
where the rxn occurs
77
Binding Site
area that holds the substrate in proper place
78
What is the effect of temp on enzyme activity?
Reduces enzyme rxn rates (usually 25-40C)
79
What is an enzyme inactive form?
Zymogen, can be activated by the removal of truncation
80
Allosteric
"other site" both positive and negative effectors
81
Enzyme induction or upregulation
increase gene expression, synthesis of more enzyme molecules
82
Repression-downregulation
decrease gene expression, decrease synthesis of enzyme molecules
83
Degradation
can be achieved by specific changes in the protein structure that is recognized from degradation by the ubiquitin-proteasome
84
What factors affect enzyme activity?
Substrate concentration, temp changes, pH changes
85
Ionic Bond
A bond between an anion and cation
86
Which AA can be phosphorylated?
Serine and Threonine and (tyrosine)
87
Which AA can have N-linked glycosyation?
Asn
88
Which AA can have O-linked glycosyaltion?
Ser and Thr
89
N-terminus
On the left, free amino acid end
90
C-terminus
On the right
91
Prosthetic group
Coenzyme that is permanently bound to an enzyme and remains unchanged after a reaction
92
Induction
increasing the amount of enzymes
93
The affinity of two different enzymes for their substrates can be compared by
Km
94
the inhibitor can bind to either the E or ES complex at a site that is not the enzymes catalytic site
noncompetitive
95
What are statin drugs?
Competitive inhibitor
96
Where does a noncompetitive inhibitor bind?
Different than the catalytic site
97
What is Km?
substrate concentration required to attain ½ maximal velocity
98
Do competitive inhibitors bind to the ES site?
NO
99
Myoglobin
Consist of many alpha helices
100
What stabilizes hemoglobin?
High pH
101
How many covalent bonds can a ferrus ring have?
6
102
What does Histidine allow Hb to do?
Regulate O2 in the blood and buffer and manage pH
103
What does the Histidine pKa do with Hb?
Changes the pKa to go closer to physiological so it gets better
104
Carbonic anhydrase
is an enzyme that speeds up CO2 dissolving in H2O
105
What does 2,3-BPG do?
1. Higher levels promote O2 release to the tissues
2. Decreases the affinity of Hb for O2
3. Negative allosteric effector
