Protein Structure and Function Flashcards
What do Proteins Do?
Structure Movement Catalysis Communication Transport
What is a Zwitterion?
A molecule with a neutral overall charge with both positive and negative charges
Draw a Generic Amino Acid at pH 7
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Charge of Generic Amino Acid at pH=1
Positive
Charge of Generic Amino Acid at pH=14
Negative
Draw a Generic Amino Acid at pH 1
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Draw a Generic Amino Acid at pH 14
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Hydrophobic Amino Acids
Ala Val Leu Ile Phe Trp Met Pro
Polar Amino Acids
Gly Ser Thr Tyr Cys Asn Gln His
Charged Amino Acids
Asp (-)
Glu (-)
Lys (+)
Arg (+)
Alanine
Smallest chiral amino acid
Aliphatic
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Valine
Aliphatic
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Leucine
Aliphatic
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Isoleucine
Isomer of leucine
Aliphatic
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Phenylalanine
Aromatic
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Tryptophan
Aromatic
Heterocyclic
Bulky
H donor
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Methionine
Honourary aliphatic
Thioether
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Proline
Aliphatic
Cyclic Structure
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Glycine
Achiral
Weakly polar
Very small
Flexible
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Serine
Hydroxyl Group
H donor
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Threonine
Hydroxyl group
H donor
Can be phosphorylated
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Tyrosine
Aromatic Hydroxyl group H donor Hydrophobic interactions Can be phosphorylated
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Cysteine
Thiol group
Forms disulphide bonds with Cys
pKa=6.5
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Asparagine
Amide group
H donor and H acceptor
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Glutamine
Carbamide group
H donor and H acceptor
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Histidine
Aromatic
Acid or base at pH=7
Proton donor/acceptor
pKa=6
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Aspartate
(-) charge Acidic H acceptor Polar pKa=4
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Glutamate
(-) charge Acidic Polar H acceptor pKa=4
Draw Glutamate
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Lysine
(+) charge Basic H donor Polar pKa=10
Draw Lysine
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Arginine
(+) charge Basic Guanido group Polar H donor pKa=12.5
Where are Polar Side Chains Found?
On protein surfaces
- interacts with water
- polar, uncharged amino acids
Where are Nonpolar Side Chains Found?
In the protein core
-minimizes interaction with water
Sense of Direction In Peptides
N-terminus to C-terminus
What is Primary Structure?
The sequence of amino acids in a polypeptide
Peptide bonds join each amino acid to the next
What are Amino Acids Called in Polypeptides?
Residues because of the removal of water
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
Polypeptide Backbone
The polymerization between amino and carboxylic groups attached to the alpha carbon of each amino acid
Primary Structure
Amino acid sequence
Secondary Structure
Alpha-helix and Beta-sheets
Tertiary Structure
3D structure
Quaternary Structure
A complex of protein molecules
Why are folding conformations limited?
Steric clash - high energy and unfavourable
Must minimize any steric conflict
Must maximize H-bonds in structures
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
Beta-sheet Structure
Multiple beta-strands are arranged side by side
Strands are joined by loops or other structures
Can be parallel or antiparallel
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
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
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
Fibrous Proteins
Insoluble in aqueous environments
Long protein filaments
Structural or connective proteins
Globular Proteins
Soluble in aqueous solutions
Fold into compact structures with nonpolar cores and polar surfaces
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
Stabilization of Tertiary Structure
Hydrophobic effect
H-bonding
Ion pairs (salt bridges)
Disulphide bridges
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
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
Ion pairs in Tertiary Structure
Electrostatic interactions between closely positioned formal charged groups
Charges will depend on the pH of the environment
Disulphide bonds in Tertiary Structure
Covalent bonds between closely positioned cysteines
Forms stabilizing cross-units for extracellular proteins
NOT found in quaternary structure
Domain
Polypeptide segment that has folded into a single structural subunit with a hydrophobic core
Motif
A short region of a polypeptide with a recognizable 3D shape
Prosthetic Group
The non-peptide component that is permanently incorporated into a protein
Apoprotein
Protein without characteristic prosthetic group
Holoprotein
Apoprotein combined with its prosthetic group
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
Function of Myoglobin
Facilitates O2 diffusion through muscle tissue
Acts as a local reserve of O2 during intense exercise
Stores O2 in aquatic animals
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
Function of Proximal Histidine
Binds heme into the heme-binding pocket and prevents oxidation of the iron atom
Function of Distal Histidine
Increases O2 binding affinity
Lowers affinity for other molecules
Increases specificity for O2
Oxygen Binding to Myoglobin
Hyperbolic Plot
Reversible
When pO2=Kd: [Mb]=[MbO2]
Function of Hemoglobin
O2 transport from lungs to tissues
Reversibly binds/releases O2
Structure of Hemoglobin
4 polypeptide chains
2 helices and 2 sheets
1 heme/polypeptide - binds 4 O2/Hb
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
Tense State
Low affinity for O2
Deoxy Hb
Larger central cavity
Relaxed State
High affinity for O2
Oxy Hb
Smaller central cavity
Allosteric Effectors
Compounds which, upon binding, alter affinity at other binding sites
Homoallosteric
The binding of the effector affects further binding of the same compound
Example of Homoallosteric Activator
O2 is a homoallosteric activator of Hb
Heteroallosteric
The binding of the effector affects further binding of a different compound
Example of Heteroallosteric Inhibitors
BPG and H+ are heteroallosteric inhibitors for O2
Allosteric Activators
Increases binding affinity
Allosteric Inhibitors
Decreases binding affinity
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
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
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
Lungs and Hb
Lungs have high ppO2 and high pH
-R state is favoured = O2 binding
Tissues and Hb
Respiring tissues have low pH and low ppO2
-T state is favoured = oxygen is released
Conservative Substitution
An amino acid is replaced by another amino acid with similar properties
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
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
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
