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Medical Cell Biology & Genetics > 1. Protein Structure > Flashcards

1. Protein Structure Flashcards

1
Q

What bond joins amino acids?

A

Covalent bond

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2
Q

What determines the folding of proteins?

A

The chemical and physical properties of the amino acid determined by the amino acid sequence

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3
Q

What is the general structure of an amino acid?

A

Central carbon atom bonded to:

  • NH2
  • COOH
  • R group
  • Hydrogen atom
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4
Q

How many amino acids are naturally found in our body?

A

20

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5
Q

What is the structure of an ionised amino acid?

A

Central carbon atom:

  • NH3+
  • COO-
  • R group
  • Hydrogen atom
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6
Q

What is an acid?

A

Proton donor

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7
Q

What is a base?

A

Proton acceptor

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8
Q

How are amino acids classified and why?

A

Based on the chemical properties of their R group as the rest of the amino acid is always the same

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9
Q

What chemical properties are used to classify an amino acid?

A

Polar/Non-polar
Hydrophilic/Hydrophobic
Acid/Basic/Neutral

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10
Q

What are the physical properties used to classify an amino acid?

A

Aromatic/Aliphatic (carbon ring present or not)

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11
Q

What determines the polarity of an amino acid?

A

The interaction of the amino acid R group with water

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12
Q

What is amino acid residue?

A

The remains of an amino acid after it has been joined by a peptide bond to form a protein

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13
Q

What does a pK value tell you?

A

How likely it is that the amino acid will be ionised

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14
Q

What is physiological pH?

A

7.4

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15
Q

If the pH of solution < pK value then the group will be…

A

protonated

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16
Q

If the pH of solution > pK value then the group will be…

A

deprotonated

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17
Q

Define the primary structure of a protein

A

The specific linear amino acid sequence of the polypeptide chain

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18
Q

Define the secondary structure of a protein

A

The local spatial arrangement of the polypeptide backbone (forms alpha helix or beta pleated sheet)

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19
Q

Define the tertiary structure of a protein

A

The overall 3D configuration of the protein

20
Q

Define the quarternary structure of a protein

A

The association between different polypeptide chains to form a multi-subunit protein

21
Q

How are peptide bonds formed?

A

Hydrolysis (abstraction of a water molecule)

22
Q

What are 4 characteristics of peptide bonds?

A
  • planar
  • rigid (cant rotate)
  • exist as trans in nature
  • bonds on either side of peptide bond can rotate
23
Q

Why are peptide bonds rigid?

A

C-N has partial double bond characteristics as C=0 bond causes delocalisation of electrons in C-N causing the bond to be slightly shorter

24
Q

What is a Psi bond?

A

C-C

25
Q

What is a Phi bond?

A

C-N

26
Q

What is the isoelectric point (pI) of a protein?

A

The pH at which there is no overall charge

27
Q

What type of proteins are present when pI > 7?

A

Basic proteins

28
Q

What type of proteins are present when pI < 7?

A

Acidic proteins

29
Q

If pH > pI the protein is…

A

deprotonated

30
Q

If pH < pI the protein is…

A

protonated

31
Q

What determines the confirmation of the polypeptide backbone?

A

The bond angle of the C-C & C-N adjacent to the peptide bond

32
Q

State 4 properties of an alpha helix structure

A
  • right handed helix structure
  • 3.6 amino acids per turn
  • trans orientated
  • hydrogen bonds between N-H & C=O (4 amino acids apart)
33
Q

What properties make it more likely for an alpha helix to form?

A
  • small hydrophobic residue
  • possible bond angle rotations
  • R group (supports specific confirmations)
34
Q

State 4 properties of beta pleated strands

A
  • fully extended confirmation (larger gap between amino acid residues)
  • trans
  • hyrogen bonding between each strand
  • 3 types of beta pleated strands
35
Q

What are the 3 types of beta pleated strands?

A
  • Anti-parallel
  • Parallel
  • Mixed
36
Q

What are anti-parallel beta pleated sheets?

A

Adjacent beta strands run parallel in opposite directions allowing hydrogen bonds to form between each layer

37
Q

What are parallel beta pleated sheets?

A

Adjacent beta strands run parallel in the same direction allowing hydrogen bonds to form between layers (weaker H bonds as theyre at an angle)

38
Q

What are mixed beta pleated sheets?

A

Adjacent strands contain a mix of anti-parallel and parallel strands

39
Q

What is the role of fibrous proteins?

A

Support
Shape
Protection

40
Q

What is the structure of fibrous proteins?

A

long strans or sheets made from a single type of repeating secondary structure

41
Q

What is the role of globular proteins?

A

Catalysis (forms enzymes)

Regulation (forms transporter molecules)

42
Q

What is the structure of globular proteins?

A

Compact shape made of several types of secondary structure

43
Q

What is the structure of collagen?

A

Fibrous protein
Alpha helix
Triple helical arrangement
Hydrogen bonding between chains

44
Q

How does the interaction of R groups with water affect the folding of water soluble proteins?

A

Polypeptides fold so hydrophobic chains are buried whilst hydrophilic chains are on the surface of the molecule as they like water interaction

45
Q

How does the polarity of proteins affect folding of the polypeptide?

A

Hydrohphilic chains buried and hydrophobic chains on cell surface membrane as hydrophobic chains want to interact with the membrane as theyre uncharged

Medical Cell Biology & Genetics (4 decks)

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