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BIOC192 > Q/A Session 1 > Flashcards

Q/A Session 1 Flashcards

1
Q

How does and aa look as a zwitterion?

A
  • Amine side is protonated

- CA is deprotonated (becoming a carboxylate)

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2
Q

Characteristics of a Non-Polar side chain

A
  • Mainly composed of hydrocarbons
  • Found in the core of the protein
  • Hydrophibobic
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3
Q

Characteristics of Polar Groups

A
  • Can either be charged or uncharged
  • If the pH changes, can become charged/uncharged
  • Surface of protein. Polar groups make the protein soluble
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4
Q

Characteristics of polar uncharged

A

-Polar groups in the side chains but uncharged at neutral pH

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5
Q

Characteristics of polar charged

A
  • An O by itself indicates negative charge

- Positive charge on the N atom indicated a negative charge

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6
Q

What is produced when a peptide bond forms?

A

Water

-Condendsation reaction

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7
Q

Whats the configuration of an aa

A

Trans, minimises steric hinderance

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8
Q

Is there rotation around a peptide bond?

A

No

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9
Q

Characteristics of peptide bond

A
  • Planar
  • Rigid
  • Linear
  • Cannot rotate
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10
Q

Psi bond (trident shaped)

A

Goes between Calpha-C

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11
Q

Phi bond (O with slash)

A

Goes between C-N

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12
Q

Formation of secondary structure is called

A

Nucleation

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13
Q

What are secondary structures stabilised by

A

What hold them together which is hydrogen bonds

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14
Q

Where do amino acid side chains point

A

Outwards from the helix

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15
Q

What are the 2 unfavourable amino acids in the alpha helix formation?

A
  • Glycine (too flexible)

- Proline (too bulky)

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16
Q

Explain the n+4 stabilising the alpha helix

A

Hydrogen bond goes between the Oxygen of Amino acid n ——– Hydrogen of amino acid n+4
O(n)—-hydrogen bond—-H(n+4)

17
Q

How many strand in a beta sheet

A

2-10

18
Q

What aa are used in turns on the beta sheets?

A
  • Glycine due to flexibility

- Proline due to naturally occurring bend

19
Q

What direction do antiparallel bond patterns tend to be (beta sheets)

A

vertical

20
Q

What direction do parallel bond patterns tend to be (beta sheets)

A

diagonal

21
Q

How are beta sheets pleated?

A

With a right hand twist

Turning clockwise

22
Q

What are tertiary structures?

A

Collection of secondary structures making a 3D sturcute

23
Q

Tertiary structures stabilised by:

A
  1. Metal ion coordination
  2. Hydrophobic interactions
  3. electrostatic interaction
  4. Hydrogen bonds
  5. Disulfide bond
24
Q

What are quaternary structures made from

A

-Made up of 2+ tertiary structures

25
Q

What are quaternary structrues held together by?

A

Weak/non covalent bonds

26
Q

What are supersecondary structures?

A

Combinations of secondary structures that form recognisable patterns

27
Q

What are domains?

A

Combinations of super secondary structures that form independently folded regions
-Have hydrophobic cores

28
Q

What is a chaperone?

A

helps to assist with correct folding by passively preventing incorrect folding

  • > no ATP required
  • > hydrophobic molecules
29
Q

What is a chaperonin?

A

Larger proteins that require ATP to function

30
Q

What is protein folding driven by?

A

Hydrophobic interactions

31
Q

What is the order of protein folding?

A
  1. Formation of secondary structures
  2. Several secondary structures come together and form super-secondary structures->domains
  3. Several domains come together and form almost tertiary
  4. Small conformational changes give final tertiary structure
32
Q

What is pka?

A

pH at which an ionisable group is 50% ionised

33
Q

Is pka for an amino group high or low?

A

High

34
Q

Is pka for a carboxyl group high or low?

A

Low

BIOC192 (4 decks)

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