ANE 610 > Module 8 > Flashcards

Module 8 Flashcards

(143 cards)

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1
Q

Proteins are the primary molecules that….

A

Carry out “work”

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2
Q

Proteins have a variety of functions, examples?

A

-scaffolding for tissues to be built on
-Transport across cell membrane
-Break down of nutritional molecules

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3
Q

Heteropolymers

A

Proteins: variety of amino acids bound by peptide bonds, creating long chains that fold into complex protein structures and dictate functions of proteins

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4
Q

Functional groups of amino acids

A

Amine group (N terminus)
Carboxylic acid group (C terminus)

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5
Q

Alpha Carbon

A

Central carbon binding Amino group, Carboxylic acid, Hydrogen, and variable R chain

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6
Q

Are Alpha carbons chiral?

A

All except Glycine (-H)

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7
Q

All biologically relevant amines have what type of configuration?

A

L

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8
Q

How to determine L or D?

A

Two ways

If 2D, amine group on the Left

If 3D, spell C-O-R-N in clockwise manner
- C: carboxyllic acid carbon
- O: Oxygen on carboxyl group
- R: Amino acid group
- N: Nitrogen on amine group

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9
Q

Why is it important to have the correct enantiomer?

A

Structure = Function
Proteins are enzymes, substrates will not be converted into products
(Lock and Key model)

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10
Q

One letter abbreviations: Arginine

A

R

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11
Q

One letter abbreviations: Alanine

A

A

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12
Q

One letter abbreviations: Asparagine

A

N

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13
Q

One letter abbreviations: Aspartic Acid (aspartate)

A

D
Think aciD

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14
Q

One letter abbreviations: Cysteine

A

C

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15
Q

One letter abbreviations: Glutamic Acid (Glutamate)

A

E

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16
Q

One letter abbreviations: Glutamine

A

Q
(Think Qlutamine)

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17
Q

One letter abbreviations:

A
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18
Q

One letter abbreviations:

A
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19
Q

One letter abbreviations: Histidine

A

H

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20
Q

One letter abbreviations: Isoleucine

A

I

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21
Q

One letter abbreviations: Leucine

A

L

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22
Q

One letter abbreviations: Lysine

A

K
(Idk maybe think Klysine lol)

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23
Q

One letter abbreviations: Methionine

A

M

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24
Q

One letter abbreviations: Phenylalanine

A

F

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25
One letter abbreviations: Proline
P
26
One letter abbreviations: Serine
S
27
One letter abbreviations: Threonine
T
28
One letter abbreviations: Tryptophan
W (Without serotonin I whine…)
29
One letter abbreviations: Tyrosine
Y
30
One letter abbreviations: Valine
V
31
Hydrophobic R side chains take which position?
Towards the center of the protein away from the aqueous environment. Not energetically favorable for hydrophobic molecules to be in polar environment.
32
Name that Amino Acid!
Glycine
33
Name that Amino Acid!
Alanine (Methyl group)
34
Name that Amino Acid!
Valine (Isopropyl group)
35
Name that Amino Acid!
Leucine (Isobutyl group)
36
Name that Amino Acid!
Aspartic acid (Deprotonated carboxylic acid group)
37
Name that Amino Acid!
Isoleucine
38
Name that Amino Acid!
Glutamic Acid (Ch2-CH2-COO-)
39
Name that Amino Acid!
Aspargine (Amine and carboxyl)
40
Name that Amino Acid!
Glutamine (Similar to asparagine but has one more methyl groups before NH2 / C=O)
41
Name that Amino Acid!
Proline (Forms a ring with itself!) Extremely rigid
42
Name that Amino Acid!
Phenylalanine Aromatic structure
43
Name that Amino Acid!
Tryptophan Benzene + cyclopentane with amine precursor to serotonin and melatonin
44
Name that Amino Acid!
Lysine (Positive charge on amine)
45
Name that Amino Acid!
Cysteine sulfhydryl on the end: frequently makes disulfide bonds!
46
Name that Amino Acid!
Methionine Thiol in middle, not great for Redox/ disulfide bonds like cysteine
47
Name that Amino Acid!
Tyrosine Catecholamine precursor Polar due to hydroxyl
48
Name that Amino Acid!
Arginine positive charge on double bonded amine Terminal amino groups
49
Name that Amino Acid!
Histidine Amine ring (Imidazole ring) + charge
50
Name that Amino Acid!
Serine Polar hydroxy group at terminal
51
Name that Amino Acid!
Threonine Hydroxyl and methyl group, Polar
52
Non-polar amino acids and properties
Proline, Methionine Hydrophobic, tucked into interior of structure
53
Aliphatic non-polar amino acids and properties
Glycine, alanine, valine, leucine, Isoleucine Non-polar, more hydrophobic due to increased carbon chain, or large ring
54
Aromatic chain Amino acids
Phenylalanine, Tryptophan, Tyrosine Non-polar/hydrophobic (Except tyrosine due to hydroxyl group)
55
Polar side chains (neutral charge)
Serine, Cysteine, Threonine, Asparagine, Glutamine Hydrophilic, positioned on the surface, form hydrogen bonds with water and other structures (like amino acids in alpha helix or beta sheets)
56
Positively charged polar amino acids
Histidine, Lysine, Arginine
57
Negatively charged polar amino acids
Aspartic acid, glutamic acid
58
Most Hydrophilic (5) in order of most to least
R, K, N, D, E
59
More Hydrophobic (5)
A, M, C, F, L, V, I
60
If pH is below the pKa value, the functional group is
Protonated
61
If pH is above the pKa value, the functional group is
Deprotonated
62
At the exact pH of the pKa value, the functional group is
50% protonated, 50% Deprotonated
63
What is the amino acid at physiological pH
Zwitterion; +charge on NH3 (protonated), - charge on COO- (Deprotonated) net charge = 0
64
Arginine pKa of side chain
12.5
65
Aspartic acid pKA of side chain
3.9
66
Cysteine side chain pKa
8.3
67
Glutamic Acid side chain pKa
4.2
68
Histidine side chain pKa
6.0
69
Lysine side chain pKa
10.0
70
Approximate pKa of alpha-COOH group
˜2
71
Approximate pKA of alpha-NH3+ group
˜9-10 (Let’s say 10)
72
What is a the isoelectric point (pI)
Is the point at which a protein carries No NET CHARGE 1/2(pKi + pKj)
73
Simple rule for pI calculations
- if AA doesn’t have an ionizable side chains, take the halfway boing between the pKA values for the backbone amino and backbone carboxyl - If an AA has a positively charged side chain, take the halfway point between the pKa values for the backbone amino and side chain pKa (H/K/R) -If an amino acid has a negatively charged side chain, take the halfway point between the pKa values for the backbone Carboxylic acid and the side chain pKa (E/D)
74
Secondary structure
Local arrangement of AA polypeptide backbone in space H-bond dependent A-helices B-sheets (pleated)
75
Primary structure of AA
Amino acid sequence in polypeptide chains Covalent bonds/peptide bonds
76
Tertiary Structure
Overall #D structure, global fold Covalent, ionic, VDW, Hydrophobic (all included)
77
Quarternary structure
Structure of proteins made up of more than one subunit/polypeptide chain Covalent, ionic, VDW, Hydrophobic (all included) Not all proteins have this structure Ex: Hgb, antibodies
78
How do you read a polypeptide sequence
N terminus to C terminus
79
Peptide bond reaction
Condensation Addition of chain with elimination of H2O
80
Which enzymes drives the peptide bond creation
Ribosomes
81
Which bonds are peptide bonds in the sequence?
Every 3rd bond
82
Peptide bond type and characteristics?
Amide bonds, limited rotation due to resonance, planar due to resonance
83
Which conformation is energetically favorable?
Trans
84
In Alpha helix (secondary structure), how many amino acids per helical turn?
3.6
85
B-sheets: 2 types
Parallel, antiparallel
86
What type of bond is critical for stabilizing secondary structures?
H-bonds
87
L-alpha-amino acids form:
Right handed alpha helix, side chains point outward
88
Which AA rarely participate in secondary structures and why?
Glycine: lack of beta carbon, very flexible and has significant rotation; rarely participates in alpha helix Proline: introduces kinks due to ring structure, rarely participates in alpha helix or Beta sheets
89
Disulfide bond type of reaction
Redox reaction
90
Why can’t Methionine create Sulfhydryl bonds
Methyl group and Sulfur in middle chain
91
Why do hydrophobic residues occupy the interior of proteins?
Free Energy (Delta G) decreases as protein folding increases making it energetically favorable; BUT Entropy (Delta S) decreases as well, so something else must contribute to protein folding
92
Protein unfolding =
Denaturation
93
Peptide bond cleavage
By hydrolysis and enzymatic activity
94
Factors causing protein denaturation?
pH, Temperature, enzymatic activity, exposure to reactive chemicals
95
Does denaturation = peptide bonds cleavage?
No
96
Two major groups of proteins based on general structure:
Fibrous, Globular
97
Fibrous protein structure:
Tertiary, elongated, narrow, filamentous
98
Fibrous protein function:
Primarily structural
99
Fibrous protein AA sequence:
Repetitive
100
Fibrous protein solubility in H2O
Low
101
Fibrous protein Stability:
Less sensitive to changes in heat, pH
102
Fibrous protein examples:
Collagen, Keratin, Elastin, Actin Keratin most important for exam; layers to form filaments, very solid, “Brick-upon-Brick”
103
Globular Protein structure:
Tertiary, round, spherical
104
Globular Protein Function:
Functional, involved in doing some kind of work that requires them to be malleable
105
Globular Protein AA sequence:
Irregular
106
Globular Protein Solubility in H2O:
High
107
Globular Protein Stability:
More sensitive to changes in heat and pH
108
Globular Protein examples:
Hemoglobin, myoglobin, immunoglobulins
109
Keratin secondary structures:
Alpha-helix (predominant in humans; hair, finger nails) Beta-sheet keratin: birds, reptiles
110
Alpha keratin forms:
Dimers through hydrophobic interactions (cross-link through cysteine disulfide bonds)
111
The more _________ the harder the keratin
Disulfide cross-links (when you burn hair or skin smell is produced by breaking of disulfide bonds)
112
Keratins are rich in _________. (Hint: AA)
Cysteines
113
How many Heme units per hemoglobin
4
114
What binds O on heme
Fe 2+ (ferrous ion)
115
Myoglobin has a _______ affinity for O2
High
116
Hgb structure
(65-kD) Heterotetramer, alpha2, beta2 (Dimer of dimers, 4 heme groups, one per monomer
117
T vs R form
T= Tense; dimers are constrained and low affinity for oxygen R= Relaxed, dynamic, higher affinity for oxygen
118
As the amount of oxygen in the system (Hgb) __________, the affinity of Hgb for oxygen __________
Increases, Increases
119
Oxyhgb dissociation curve shape:
Sigmoidal (indicates cooperative binding)
120
curve for myoglobin shape
Hyperbolic
121
2,3 BPG _______ affinity of Hgb
Decreases (shift to the right)
122
Why does 2,3 BPG shift curve to the right?
Negative heterotrophic allosteric effector Binds to Hgb at distant (allosteric) site and is negatively charged
123
Why is 2,3-BPG essential for proper function of Hgb?
Allows Hgb to give up O2 in peripheral tissues where PaO2 is low
124
Increased CO2 shifts curve to the ______ because it ________ affinity for oxygen
Right, decreases
125
Fetal Hgb different how?
Higher affinity for oxygen
126
Sickle cell point mutation
E6V Valine instead making structure more rigid
127
Aberrant enzymes =
Disease
128
What do enzymes do?
-Increase reaction rates (lower activation energy) -Allow reaction to proceed under milder conditions -Increase reaction specificity (provide active site for substrate) -Provide capacity for control
129
Are enzymatic processes reversible?
Mostly
130
Other names for active site?
Orthosteric, orthotopic
131
Apoenzyme means
Enzyme alone, inactive state
132
Holoenzyme means:
Enzyme with cofactor/conenzyme (AKA ready to go)
133
Coenzymes are:
Organic molecules, vitamins often coenzymes
134
Vitamin B1:
Thiamine (Thiamine pyrophosphate as coenzyme)
135
B2 Vitamin
Riboflavin (Coenzyme name FMN, FAD)
136
B3
Niacin (NAD, NADP)
137
B5
Pantothenic Acid (Coenzyme name CoA)
138
B6
Pyridoxone (coenzyme name pyridoxal phosphate)
139
B7
Biotin (Biotin as coenzyme name)
140
B9
Folate/Folic acid (tetrahydrofolate as coenzyme name)
141
B12
Cobalamin (Methylcobalamin)
142
Vit C
Ascorbic acid (Ascorbic acid as coenzyme)
143
Water soluble vitamins are often ________ of coenzymes
Precursors
ANE 610
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