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Molecules And Cells > Protein Structure > Flashcards

Protein Structure Flashcards

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Organic Chemistry 101 flashcards
1
Q

What is primary structure?

A

Base order of amino acid sequence.

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2
Q

What is a residue?

A

A single unit that makes up a polymer e.g. an amino acid

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3
Q

What is classified as a short chain and what is name given?

A

Less than 30 residues. Ogliopeptide.

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4
Q

What is classified as along chain and what name is given?

A

Between 200 -500 amincacids. Polypeptide.

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5
Q

Explain general peptide bonding:

A
  1. all atoms of peptide bond lie in same plane
    due to resonance.
  2. Double carbon bond prevents free rotation.
  3. Average bond length is 1.33 angstroms.
  4. Bond angles tend to be near 110º.
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6
Q

How are amino acids measured?

A

In angstroms.
1 A = 0.1nm

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7
Q

Explain peptide bond formation:

A
  1. Carbon in carbonyl group bonds with nitrogen in amino group.
  2. Electrons in bond are delocalized causing peptide bond to resist further rotation.
  3. Read from n terminus
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8
Q

Which amino acids are hydrophobic / non-polar?

A

Glycine, alanine, valine, proline, leucine, isoleucine, methionine and phenylalanine

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9
Q

Which amino acids are polar?

A

Tyrosine, tryptophan, asparagine, glutamine, cysteine, serine and threonine.

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10
Q

Which amino acids are charged?

A

Histidine, asparatate, glutamate, arginine and lysine

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11
Q

Which amino acid is able to form a disultide bond?

A

Cysteine

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12
Q

Explain the forms amino acids come in:

A

L isomer and D isomer which are mirror images.

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13
Q

Which isomer is in proteins?

A

L isomers only

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14
Q

How many amino acids in a protein?

A

Between 50 - 2000

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15
Q

Explain trans and cis configuration of peptide bond:

A

In trans configuration, C-alpha atoms are on opposite sides of the peptide bond.
In cis configuration, C-alpha atoms are on the same side of the peptide bond.

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16
Q

Which configuration is preferred and why?

A

Trans configuration.
Steric clashes occur affecting the structure and properties.

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17
Q

What is secondary structure?

A

Organised regions of polypeptide backbone, stabilised by hydrogen bonds between atoms.

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18
Q

What are the 3 structures?

A

Alpha helix.
Beta sheet.
Beta turn.

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19
Q

Describe and explain the alpha helix structure:

A

Forms a spiral structure.
Hydrogen bonds form between carboxylate oxygen and amide hydrogen.
All backbone aa are bonded to each other except first and last aa.
Side chains point outwards.

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20
Q

Describe and explain the beta sheet structure:

A

Consists of laterally packed beta strands.
Strands between 5-8 aa.
H bonds form perpendicular to strand.
Side groups stick out above and below plane.
Sometimes curve round to form beta barrel.

21
Q

Describe and explain beta turn structure:

A

Occurs when protein needs to change direction.
Composed of 4 residues.
Form sharp u-bends.
Located on surface of protein
Often stabilised by h bonds form between between end residues.
Helps long pp fold into complex structures.

22
Q

What determines the secondary structure?

A

Mostly determined by primary sequence.
Can be influenced by long-range interactions.

23
Q

What is a structural motif?

A

A particular combination of 2 + secondary structures that form a distinct SD structure appearing in multiple proteins.

24
Q

Give an example of a structural motif:

A

Alpha helix based coiled coil.

25
Q

Describe the structure of alpha helix coiled coil:

A

Alpha helixes from 2-4 pp chains coil about one another.
Due to strip of aliphatic side chains interacting with each other.

26
Q

What is a sequence motif?

A

A pattern of amino acids in a continuous segment of a protein.
Repeated in many proteins or many times within one protein.

27
Q

What is tertiary structure?

A

3D arrangement of amino acid residues.

28
Q

Which amino acid can for disulphide bonds?

A

Cystine.

29
Q

How do covenant bonds affect structure?

A

Increases stability.

30
Q

How do hydrophilic amino acids affect structure?

A

Increase solnability.

31
Q

Outline the characteristics of globular proteins:

A

Spherical 3D structure.
Consists of helices, beta turns and other molecules.
No symmetry.

32
Q

Outline the key characteristics of fibrous proteins:

A

Extended structure about 100nm or more.
Imperfect heptad repeat (7 aa).
Provide structural support.

33
Q

Describe an example of a fibrous protein:

A

3 pp chains wind around eachother to form a superhelical cable.
H bonds form between strands.
Glycine appears at every 3 residues.

34
Q

What is quaternary structure and its purpose?

A

Interaction of 2 app chains.
Typically held together by non-covelantbonds.
Increases efficiency of sequential proteins.

35
Q

What is a supramolecular complex?

A

Tens to hundreds of pp chains interacting.

36
Q

What is the purpose of supramolecular complexes?

A

Carry out complex cellular processes by integrating multiple proteins with distinct functions into one large assembly.
E.g. Nucleic pore + ribosomes.

37
Q

What is a protein family?

A

Proteins with related shapes.
Will have similar stretches of amino acids.

38
Q

What is the purpose of post translational modification?

A

Alters physical and chemical properties increasing diversity, conformation and binding capacity.

39
Q

State 3 structural folding limitations:

A
  1. Amino acids can only bind with opposite groups (carbonyl x amide).
  2. Pp chain can only rated around peptide band with specific angles.
  3. Limited number of angles possible as backbone ur side chain atoms would come too close together.
40
Q

State protein folding paradox:

A

Each aa has about 10 conformations.
For a protein with 124aa, there will be 10^124 possible structures.
However is able to fold in less than a second.

41
Q

Explain nucleation condensation model:

A

Neighbouring residues in sequence form native secondary structure acting as nucleus so native structure would propagate in a stepwise manner.
Therefore tertiary structure form as consequence.

42
Q

Explain co-translational folding:

A

Start to told while being synthesised.
Increases efficiency and decreases chance of mistolding.

43
Q

Define a buffer:

A

Resists changes in pH.
Conjugate base and weak acid or conjugate acid and weak base.

44
Q

Is amino group protonated or deprotonated.

A

Protonated.

45
Q

Is carbonyl group protonated or deprotonated.

A

Deprotonated.

46
Q

What is the pKa value?

A

Susceptibility of a proton to removal by reaction with a base.

47
Q

Which r groups do not ionise?

A

Aspartic, glutamic, arginine, lysine and histidine.

48
Q

What is the protein isoelectric point (pi)?

A

Protein has net charge zero.

49
Q

What are the stages of purification?

A
  1. Salting out: less solvable at high salt conc.
  2. Dialysis: semipermeable.
  3. Filtration: separation on basis of size.
  4. Ion-exchange chromatography: separation on basis of charge.
  5. Affinity chromatography: separation on basis of target binding.

Molecules And Cells (2 decks)

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