Proteins Flashcards
1
Q
Amino Acid Stereochemistry
A
- L and D enantiomers in every amino acid except glycine
- racimisation (conversion) possible
- only L amino acids found in humans
2
Q
Peptide Bond
A
- condensation reaction between amino group and carboxyl group of two amino acids
- forms polypeptide chain
3
Q
Peptide Bond Chemistry
A
- partial double bond character formed by electron sharing (resonance) between O, C, and N
- this means the bond is planar and polar (oxygen has a partial negative charge and nitrogen has a partial positive charge)
4
Q
Peptide Bond Configurations
A
- bonds between amino group/a carbon and a carbon/carbonyl are single and can rotate
- two torsion angles
- phi (N-C)
- psi (C-C)
- gives cis trans isomerism
- trans form preferred as the the alpha carbons are on opposite sides of the bond and therefore there is less steric clash
5
Q
Amino Acid Side Chain Configuration
A
- aliphatic
- non polar
- aromatic
- polar
- charged
6
Q
Peptide Bond and Protein Folding
A
- unfolded polypeptide exists are a random mixture of many conformations and this has high entropy
- rigidity of peptide unit and restricted set of allow torsion angles limits the number of structures accessible to the unfolded form sufficiently to allow protein folding to take place
7
Q
Types of Amino Acids
A
- essential amino acids: required in our diet for synthesis
- standard amino acids (20)
- protein amino acids
8
Q
Ramachandran Plot
A
- gives all possible psi and phi angle combinations
- based on which rotations don’t come closer than the sum of the VDW radii
- indicates which are preferred and allowed
9
Q
a helix
A
- peptide bonds are polar so hydrogen bonds can form
- extremely favorable configurations
- dipoles of H bonding backbone core are in perfect alignment
- helix radius allows favorable VDW interactoins
10
Q
B sheet
A
- hydrogen bonded B strands
- anti-parallel or parallel strands
- anti parallel more favorable
- very favorable interactions
11
Q
Regular Secondary Structure
A
- conserves the planar peptide bond (ideal geometry)
- ideal VDW interactions (Ramachandran plot)
- H bonding available (ideal)
- regular and repeating units
- local conformation (torsion angles)
12
Q
Acidic Amino Acids
A
- glutamic acid and aspartic acid
- side chains are negative
- use Henderson Hasselbach equation
13
Q
Basic Amino Acids
A
- lysine and arginine
- side chains are positive
14
Q
Keratin
A
- haptoid repeat (repeating position on helix)
- super secondary structure: coiled coil
- 3 helices associated
- non polar side chains drive association (amphipathic molecules)
- hydrophobic effect
15
Q
Fibroin
A
- anti parallel B sheet
- repeat structure of glycine-alanine
- close packing
- side chains of residues associate on the same layer to give differing widths
16
Q
Tertiary Structure
A
- super secondary interactions
- hydrophobic interactions
- VDW interactions
- 3D arrangment of all atoms
- ‘folding’
17
Q
Amino Acid Side Chain Packing in Protein Core
A
- non polar aliphatic amino acids found inside the protein closely packed
- spherical packing in protein fills up most of the space
- VDW interactions hold protein together when folded
- hydrophobic effect helps this
- aromatic amino acids are hydrophobic and contribute to this folding
- side chain packing against each other with non covalent interactions hold the shape
18
Q
Glycine
A
- different Ramachandran plot
- side chain of H
- therefore, no steric clash between a carbon and b carbon so more positions are possible
- glycine facilitates turns in proteins
- fits in small spaces/tight turns
19
Q
Collagen
A
- Extended coiled coil
- glycine residues used to fit inside tightly coiled helix
- sequence is glycine every 3rd amino acid
20
Q
Proline
A
- ring means it has a completely fixed structure so counteracts glycine’s flexibility
21
Q
Sulfur containing Amino Acids
A
- cysteine
- post-translational modification gives cystine
- sulf-hydryyl group undergoes oxidation and loss of 2 H ions
- forms covalent disulfide bond
- cysteine residues found in cytoplasm
- disulfide bonds are secreted via secretory pathway
- methionine
- methio-ester group
- only linear side chain
22
Q
Protein Folding
A
Random coil: no tertiary structure/protein denatured
Native: folded with tertiary structure
Protein folding has G = -50 kj/mol so is slightly energetically favorable
23
Q
Oligomeric structure
A
- 2 or more polypeptides coming together to form a protein
- subunit = one polypeptide in an oligomeric protein
- monomeric/dimeric/trimeric/oligomeric
- homodimer - identical units
- heterodimer - different units
24
Q
Quaternary Structure
A
- long range interactions stabilise protein structures
25
Q
Multi Domain Proteins
A
- modular proteins
- multiple units associate with coils or turns
- each individual domain can fold on its own
- can be flexible
26
Q
Post Translational Modification
A
- reversible modification
- serine + phosphoric acid is a condensation reaction with product of phosphopserine
- irreversible modification
- glutamic acid transformed into carboxyglutamic acid
27
Q
Ligand
A
- molecule binding reversibly to form a protein complex
eg. hemoglobin and oxygen
28
Q
Dissociation Constant
A
- low Kd = high affinity = tight binding
29
Q
Myoglobin
A
- can bind with oxygen or CO
- competition for dissociated state of protein
30
Q
Histidine
A
- aromatic and basic amino acid
- 80% unprotonated
31
Q
Oxygen Binding to Myoglobin
A
- one sigma, one pi , and one anti pi bond formed
- free electrons used to bind iron ion
- myoglobin has a distal and proximal histidine ring
- iron is in a porphoryn rring
- because the unshared electrons are in the side orbitals of oxyen, there is a bonding that is compatible with the position of the distal histidine
32
Q
Heme in Myoglobin
A
- iron has an octahedral coordination
- 6 atoms around it with electrons pointing towards in
- porphyrin ring becomes a heme group with iron ion
- interacts with unshared electrons on N
33
Q
Carbon Monoxide Binding to Myoglobin
A
- extremely high affinity for heme
- dipolar molecule
- distal histidine means molecule must tip to fit in and this is a less favorable bond angle
- CO is a planar molecule
- weaker binding
34
Q
Allostery
A
- protein can take on different shapes
- these shape changes are conformational changes
35
Q
Cooperativity
A
- one subunit changes shape causing a second subunit to change as well
36
Q
Electronic Properties of Iron
A
- 3+ : ferric iron
- 2+ : ferrous iron
37
Q
Effect of Ligands on D orbitals of iron
A
- head on overlap of electrons is not favorable
- the interaction with histidine means that some orbitals will be unfavorable
- orbitals that point towards ligand electrons are not allowed (2 of 5)
38
Q
D orbital split
A
- iron + heme: more favorable to spread out bc energy gap is so low
- iron + Mb: high spin orbitals filled (high spin orbitals have axial positions)
iron + MbO: low spin orbitals filled (large energy gap between the two orbitals) - energy gap increases too much so lower energy orbitals are filled preferentially
39
Q
Oxygen Binding + Conformational Changes
A
- iron sites below the place to decrease N overlap in high spin conformation
- addition of oxygen collapses electrons into lower orbitals not pointing towards the iron so it becomes level
low spin conformation - this causes the proximal histidine to move up
- the attached F helix moves up as well
40
Q
Quaternary Structure of Hemoglobin
A
- two alpha and two beta subunits
41
Q
Cyclin Dependent Protein Kinases
A
- phosphorylation by ATP
- Thr160 phosphorylated and activated
- without phosphate there is a attraction between the E162 and R150 residues
- with phosphate there is a conformational change, ie. a rotation of a section of the polypeptide
- this conformational change can lead to a blocking or unblocking of the active site for example
42
Q
Proteolysis
A
- protease enzymes
- trypsinogen > trypsin
- chymotrypsinogen > chymotrypsin (by trypsin enzyme)
43
Q
Zymogens
A
Inactive forms of enzymes
44
Q
Chymotrypsin
A
- critical cleavage of Ser14 and Arg15 residues
- cleavage leaves a free a NH3 that becomes protonated
- D 194 negatively charged aspartic acid interacts with Ile 16 with a positive charge
- conformational change (swing around)
- active site changes shape because of this interaction that stabilizes the active enzyme
45
Q
Protein Motifs
A
- simple combinations of a few secondary structure elements with a specific geometric arrangement
- are not complete structures
- can have a conserved sequences
46
Q
Examples of Protein Motifs
A
- helix loop helix
- zinc finger
- EF hand
- 4 helix bundle
- greek key
- B a B motif
47
Q
Helix loop Helix
A
- simple motif
- binds to motor groove of DNA
48
Q
Zinc Finger Domain
A
- a helix and a small region of anti parallel B sheet
- Zn coordinated by 2 Cys residues and 2 His residues
- controls cell response to blood flow changes
- DNA binding protein
49
Q
4 Helix Bundle
A
- 4 helices and 3 short loops
- helices associate because of residue distribution
- hydrophobic residues orientate inwards
50
Q
EF Hand Motif
A
- type of helix loop helix
- specific for Calcium ion binding
- loop binds Ca
- side chain/main chain involved in coordinating meta
51
Q
Greek Key Motif
A
- found in proteins with anti parallel B sheets
- 4 adjacent antiparallel stranfs
- no particular function
52
Q
B a B motifs
A
- found in almost every structure with parallel B sheets
- a helix connects C terminus of one B strand with the N terminus of a second
- every B a B contains 2 B strands, 2 loop regions, and one a helix
- can be found in larger repeating domains
53
Q
Leucine Rich Repeat Domains
A
- repeating units of B a B motifs
- curves into a horseshoe shape
- parallel B strands
54
Q
Protein Domains
A
- proteins can be multidomains
- this may aid in folding
- most proteins are made of more than one domain
