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biological chemistry > Proteins > Flashcards

Proteins Flashcards

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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
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2
Q

Peptide Bond

A
  • condensation reaction between amino group and carboxyl group of two amino acids
  • forms polypeptide chain
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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)
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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
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5
Q

Amino Acid Side Chain Configuration

A
  1. aliphatic
  2. non polar
  3. aromatic
  4. polar
  5. charged
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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
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7
Q

Types of Amino Acids

A
  1. essential amino acids: required in our diet for synthesis
  2. standard amino acids (20)
  3. protein amino acids
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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
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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
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10
Q

B sheet

A
  • hydrogen bonded B strands
  • anti-parallel or parallel strands
  • anti parallel more favorable
  • very favorable interactions
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11
Q

Regular Secondary Structure

A
  1. conserves the planar peptide bond (ideal geometry)
  2. ideal VDW interactions (Ramachandran plot)
  3. H bonding available (ideal)
    - regular and repeating units
    - local conformation (torsion angles)
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12
Q

Acidic Amino Acids

A
  • glutamic acid and aspartic acid
  • side chains are negative
  • use Henderson Hasselbach equation
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13
Q

Basic Amino Acids

A
  • lysine and arginine

- side chains are positive

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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
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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
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16
Q

Tertiary Structure

A
  • super secondary interactions
  • hydrophobic interactions
  • VDW interactions
  • 3D arrangment of all atoms
  • ‘folding’
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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
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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
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19
Q

Collagen

A
  • Extended coiled coil
  • glycine residues used to fit inside tightly coiled helix
  • sequence is glycine every 3rd amino acid
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20
Q

Proline

A
  • ring means it has a completely fixed structure so counteracts glycine’s flexibility
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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
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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
  1. helix loop helix
  2. zinc finger
  3. 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

biological chemistry (7 decks)

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