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BIOC192 2024 > Lecture 4 > Flashcards

Lecture 4 Flashcards

Building blocks of proteins

1
Q

How many different amino acids are there?

A

20

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2
Q

What do amino acids contain?

A

Basic amino group, acidic carboxyl group

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3
Q

The alpha carbon of an amino acid is a…?

A

Chiral compound

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4
Q

Define chirality

A

Non-superimposable mirror images on a compound

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5
Q

Amino acids act as __ in solution

A

Zwitterions

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6
Q

Define a zwitterion

A

An ion existing with a +ve and -ve charge at the same time

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7
Q

Amino acids differ by…?

A

Their side chain (R group)

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8
Q

What are the four classes of amino acid?

A

Non-polar, Polar uncharged, Polar positive, Polar negative

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9
Q

What is the water associated nature structure of most proteins?

A

Hydrophobic (non-polar) group gets buried within the core in order to stabilise the protein. Hydrophilic (polar) group lies on the exterior

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10
Q

Why is the hydrophilic component of a protein generally exposed?

A

It requires energy to bury a charge. It is tied up with salt links and H-bonds as well as residues of oppositely charged residues to neutralise the charge

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11
Q

What is different about glycine?

A

It is not chiral as it’s side chain is a singular H, this makes is relatively flexible

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12
Q

What is different about Proline?

A

Side chain bonds back to the main chain N forming an imino acid which is much more rigid

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13
Q

What are the name forms that amino acids exist as?

A

three and one letter abbreviations

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14
Q

Why are one letter abbreviations useful?

A

Helps to describe sequence alignment and mutations

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15
Q

What does ‘E6V’ mean?

A

There is a mutation of glutamate to a valine at position 6 in the protein sequence

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16
Q

What amino acids can act as acids and bases?

A

Amino acids with ionisable side chains where a proton can be donated or accepted

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17
Q

What is pKa

A

the pH at which the group is 50% ionised

18
Q

What is pL

A

the pH at which the net charge on a amino acid is zero (isoelectric point)

19
Q

What is the general pKa values for the carboxyl and amino groups respectively?

A

~2 and ~10

20
Q

What are modified amino acids?

A

Amino acid derivatives that are created in-house

21
Q

What is translation?

A

The translation of RNA to proteins at the ribosome

22
Q

What is ‘post-translational modification’

A

When the amino acid is modified after they are added to a protein

23
Q

What is an example of post-translational modification?

A

The disulphide bond

24
Q

What are some other amino acid modifications?

A

Phosphorylation, hydroxylation, carboxylation, metal binding, iodination, glycosylation

25
Q

What is phosphorylation?

A

Addition of phosphate or phosphate containing group

26
Q

What is phosphorylation used for?

A

To control enzyme activity (ON/OFF switch)

27
Q

What is hydroxylation used for?

A

needed to prevent connective tissue diseases and scurvy (often proline and lysine involved)

28
Q

What is carboxylation used for?

A

blood clotting (often glutamate)

29
Q

What is glycosylation?

A

Addition of sugars

30
Q

What is the peptide bond?

A

The covalent bond between amino acids to form chains of peptides / proteins

31
Q

What occurs when the peptide bond is formed?

A

Carxoyl - amino water is removed leaving a ‘residue’

32
Q

What is the shape of the peptide bond?

A

Planar

33
Q

Why is the peptide bond planar?

A

maximised pi bonding overlap

34
Q

What is the bond order character of a peptide bond?

A

40% double bond

35
Q

What is the rotational barrier of a peptide bond?

A

~80kJ/mol

36
Q

What creates the dipole in a peptide bond?

A

The C=O which is partial -ve and N-H which is partial +ve

37
Q

What is a peptide?

A

A short stretch of amino acids joined by peptide bonds

38
Q

What is a protein

A

A longer chain of amino acids joined together by peptide bonds, usually with a biological function

39
Q

What are peptides or proteins constructed of?

A

Amino acid residues

40
Q

What is the purpose of the side chain?

A

To determine and carry out protein function

BIOC192 2024 (25 decks)

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