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BIOCH 200 > Protein Structure and Function > Flashcards

Protein Structure and Function Flashcards

1
Q

What do Proteins Do?

A 
Structure
Movement
Catalysis
Communication
Transport
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2
Q

What is a Zwitterion?

A

A molecule with a neutral overall charge with both positive and negative charges

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3
Q

Draw a Generic Amino Acid at pH 7

A

See Cheat Sheet

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4
Q

Charge of Generic Amino Acid at pH=1

A

Positive

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5
Q

Charge of Generic Amino Acid at pH=14

A

Negative

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6
Q

Draw a Generic Amino Acid at pH 1

A

See Cheat Sheet

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7
Q

Draw a Generic Amino Acid at pH 14

A

See Cheat Sheet

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8
Q

Hydrophobic Amino Acids

A 
Ala
Val
Leu
Ile
Phe
Trp
Met
Pro
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9
Q

Polar Amino Acids

A 
Gly
Ser
Thr
Tyr
Cys
Asn
Gln
His
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10
Q

Charged Amino Acids

A

Asp (-)
Glu (-)
Lys (+)
Arg (+)

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11
Q

Alanine

A

Smallest chiral amino acid

Aliphatic

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12
Q

Draw Alanine

A

See Cheat Sheet

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13
Q

Valine

A

Aliphatic

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14
Q

Draw Valine

A

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15
Q

Leucine

A

Aliphatic

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16
Q

Draw Leucine

A

See Cheat Sheet

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17
Q

Isoleucine

A

Isomer of leucine

Aliphatic

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18
Q

Draw Isoleucine

A

See Cheat Sheet

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19
Q

Phenylalanine

A

Aromatic

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20
Q

Draw Phenylalanine

A

See Cheat Sheet

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21
Q

Tryptophan

A

Aromatic
Heterocyclic
Bulky
H donor

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22
Q

Draw Tryptophan

A

See Cheat Sheet

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23
Q

Methionine

A

Honourary aliphatic

Thioether

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24
Q

Draw Methionine

A

See Cheat Sheet

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25
Proline
Aliphatic | Cyclic Structure
26
Draw Proline
See Cheat Sheet
27
Glycine
Achiral Weakly polar Very small Flexible
28
Draw Glycine
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29
Serine
Hydroxyl Group | H donor
30
Draw Serine
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31
Threonine
Hydroxyl group H donor Can be phosphorylated
32
Draw Threonine
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33
Tyrosine
``` Aromatic Hydroxyl group H donor Hydrophobic interactions Can be phosphorylated ```
34
Draw Tyrosine
See Cheat Sheet
35
Cysteine
Thiol group Forms disulphide bonds with Cys pKa=6.5
36
Draw Cysteine
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37
Asparagine
Amide group | H donor and H acceptor
38
Draw Asparagine
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39
Glutamine
Carbamide group | H donor and H acceptor
40
Draw Glutamine
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41
Histidine
Aromatic Acid or base at pH=7 Proton donor/acceptor pKa=6
42
Draw Histidine
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43
Aspartate
``` (-) charge Acidic H acceptor Polar pKa=4 ```
44
Draw Aspartate
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45
Glutamate
``` (-) charge Acidic Polar H acceptor pKa=4 ```
46
Draw Glutamate
See Cheat Sheet
47
Lysine
``` (+) charge Basic H donor Polar pKa=10 ```
48
Draw Lysine
See Cheat Sheet
49
Arginine
``` (+) charge Basic Guanido group Polar H donor pKa=12.5 ```
50
Where are Polar Side Chains Found?
On protein surfaces - interacts with water - polar, uncharged amino acids
51
Where are Nonpolar Side Chains Found?
In the protein core | -minimizes interaction with water
52
Sense of Direction In Peptides
N-terminus to C-terminus
53
What is Primary Structure?
The sequence of amino acids in a polypeptide | Peptide bonds join each amino acid to the next
54
What are Amino Acids Called in Polypeptides?
Residues because of the removal of water
55
Properties of Primary Structure
Rigid and planar = partial double bond character stabilizes bond - no rotation around C-N bond Electrons in peptide bonds are somewhat delocalized, generating two resonance forms Functional groups in peptide bonds are potential H-bond acceptors or donors
56
Polypeptide Backbone
The polymerization between amino and carboxylic groups attached to the alpha carbon of each amino acid
57
Primary Structure
Amino acid sequence
58
Secondary Structure
Alpha-helix and Beta-sheets
59
Tertiary Structure
3D structure
60
Quaternary Structure
A complex of protein molecules
61
Why are folding conformations limited?
Steric clash - high energy and unfavourable Must minimize any steric conflict Must maximize H-bonds in structures
62
Alpha-helix Structure
Carbonyl oxygen of each residue forms an H-bond with the backbone -NH group Core composed of backbone - no side chains Complete H-bond satisfaction Handedness doesn't change with orientation Residues 3-4 apart in the primary structure are close in the secondary structure
63
Beta-sheet Structure
Multiple beta-strands are arranged side by side Strands are joined by loops or other structures Can be parallel or antiparallel
64
Stabilizing Forces in Secondary Structure
``` Alpha-helix = H-bonds between backbone CO and NH groups in same helices Beta-sheet = H-bonds between backbone CO and NH groups of neighbouring strands ```
65
Irregular Secondary Structure
Helices and sheets are regular secondary structure -the backbone has the same configuration for every amino acid Elements of regular secondary structure are linked by irregular ones NOT DISORDERED
66
Tertiary Structure Characteristics
Arrangement of atoms in a single polypeptide -arrangement of secondary structure in relation to each other -positions of amino acid side chains -prosthetic groups Can be fibrous or globular
67
Fibrous Proteins
Insoluble in aqueous environments Long protein filaments Structural or connective proteins
68
Globular Proteins
Soluble in aqueous solutions | Fold into compact structures with nonpolar cores and polar surfaces
69
Hydrophobic Interactions in Globular Proteins
Hydrophobic side chains = interior of globular protein Hydrophilic side chains = surface of globular protein Irregular structure on the surface of globular proteins =interact with solvent
70
Stabilization of Tertiary Structure
Hydrophobic effect H-bonding Ion pairs (salt bridges) Disulphide bridges
71
Hydrophobic effect in Tertiary Structure
The shape of globular proteins depends on relative positions of hydrophobic amino acids in the proteins primary structure Driving force via which soluble proteins adopt and maintain their tertiary structure
72
H-bonding in Tertiary Structure
Weak forces between closely positioned polar side chains = fine-tunes and stabilize secondary and tertiary structure Also forms between backbone groups and side chains
73
Ion pairs in Tertiary Structure
Electrostatic interactions between closely positioned formal charged groups Charges will depend on the pH of the environment
74
Disulphide bonds in Tertiary Structure
Covalent bonds between closely positioned cysteines Forms stabilizing cross-units for extracellular proteins NOT found in quaternary structure
75
Domain
Polypeptide segment that has folded into a single structural subunit with a hydrophobic core
76
Motif
A short region of a polypeptide with a recognizable 3D shape
77
Prosthetic Group
The non-peptide component that is permanently incorporated into a protein
78
Apoprotein
Protein without characteristic prosthetic group
79
Holoprotein
Apoprotein combined with its prosthetic group
80
Structure of Heme
Circular and planar The porphyrin ring contains a Fe2+ ion coordinated between the four N atoms Two substituents at the bottom of the ring are polar charged propionyl groups - the rest are non-polar aliphatic
81
Function of Myoglobin
Facilitates O2 diffusion through muscle tissue Acts as a local reserve of O2 during intense exercise Stores O2 in aquatic animals
82
Structure of Myoglobin
``` Single polypeptide 8 helices and irregular structure Heme prosthetic group Hydrophobic pocket between helix E and F Polyphyrin ring held in place by hydrophobic interactions and by a coordination bond between Fe2+ and a proximal histidine ```
83
Function of Proximal Histidine
Binds heme into the heme-binding pocket and prevents oxidation of the iron atom
84
Function of Distal Histidine
Increases O2 binding affinity Lowers affinity for other molecules Increases specificity for O2
85
Oxygen Binding to Myoglobin
Hyperbolic Plot Reversible When pO2=Kd: [Mb]=[MbO2]
86
Function of Hemoglobin
O2 transport from lungs to tissues | Reversibly binds/releases O2
87
Structure of Hemoglobin
4 polypeptide chains 2 helices and 2 sheets 1 heme/polypeptide - binds 4 O2/Hb
88
Oxygen Binding to Hemoglobin
O2 at the 6th coordination position of a Fe2+ ion in a heme ring His F8 (proximal) and His E7 (distal) don't change position Sigmoidal binding curve -cooperative binding affinity -reflects a change in binding affinity
89
Tense State
Low affinity for O2 Deoxy Hb Larger central cavity
90
Relaxed State
High affinity for O2 Oxy Hb Smaller central cavity
91
Allosteric Effectors
Compounds which, upon binding, alter affinity at other binding sites
92
Homoallosteric
The binding of the effector affects further binding of the same compound
93
Example of Homoallosteric Activator
O2 is a homoallosteric activator of Hb
94
Heteroallosteric
The binding of the effector affects further binding of a different compound
95
Example of Heteroallosteric Inhibitors
BPG and H+ are heteroallosteric inhibitors for O2
96
Allosteric Activators
Increases binding affinity
97
Allosteric Inhibitors
Decreases binding affinity
98
Events in O2 binding to Hb
T state = no O2 bound - O2 binds to a subunit - Fe2+ moves into plane of heme - His F8 moves with iron - Helix F moves - Subunit interface changes - Subunit interface changes affects other subunits - Helix F/His F8/Fe2+ movement - O2 binding site becomes high affinity - O2 binds more readily to other binding sites
99
What Happens When BPG Binds to Deoxyhemoglobin
BPG is essential for the formation of the T state BPG binds to the central cavity of deoxyhemoglobin The (-) charges on BPG interact with the (+) charged groups on the protein that are directed into the central cavity The central cavity in oxyhemoglobin is too small to accommodate BPG
100
Hydrogen Ions and Hb
Protons lower pH Lowering pH leads to protonation of side chains and functional groups Groups associated with BPG binding become protonated -enhance BPG binding -reduce O2 binding Bohr Effect
101
Lungs and Hb
Lungs have high ppO2 and high pH | -R state is favoured = O2 binding
102
Tissues and Hb
Respiring tissues have low pH and low ppO2 | -T state is favoured = oxygen is released
103
Conservative Substitution
An amino acid is replaced by another amino acid with similar properties
104
Critical Substitution
An amino acid is replaced by another amino acid with different properties - sickle cell anemia = disastrous genetic disease - fetal hemoglobin = physiologically significant adaptation
105
Sickle Cell
In Hb, a small hydrophobic surface patch is expelled between the E and F helices during the transition from R to T Hydrophobic Val binds and causes the Hb molecules to aggregate
106
Fetal Hemoglobin
2 alpha and 2 gamma subunits -gamma subunit is homologous with the beta subunits Sub of His 143 with serine -His 143 is involved in binding BPG -decreased BPG affinity, increased O2 affinity

BIOCH 200 (9 decks)

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