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BIOC192 2024 > Lecture 4 - Building Blocks of Proteins: Amino Acids > Flashcards

Lecture 4 - Building Blocks of Proteins: Amino Acids Flashcards

1
Q

What do all amino acids contain:

A

An alpha carbon, Amino group, Carboxyl group, Side (R) Chain

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2
Q

An alpha carbon with 4 different groups is called what?

A

Chiral

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3
Q

What forms can amino acids exist in?

A

L or D (predominantly L form)

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4
Q

What are enantiomers?

A

Non-superimposable mirror images

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5
Q

What is the predominant form of amino acids in solution?

A

Zwitterion (COOH deprotonated and NH2 protonated)

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6
Q

What are common in the 20 amino acids?

A

The backbone

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7
Q

What are different in the 20 amino acids?

A

The side chains

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8
Q

What does each amino acid have (naming)

A

A full name, abbreviated 3 letter name, 1 letter name.

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9
Q

What do the amino acids have due to their different side chains?

A

Different chemical properties

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10
Q

What do amino acid side chains do in proteins?

A

Carry out the biochemical reactions for which proteins are known

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11
Q

How are amino acids classified?

A

Based on their chemical properties

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12
Q

What are most non-polar amino acids?

A

Hydrophobic

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13
Q

Where are hydrophobic amino acids found?

A

Typically on the inside of a protein stabilising the structure (forming the hydrophobic core)

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14
Q

What is glycine’s R group?

A

A hydrogen making it non-chiral, flexible because its R group is small meaning it is found in regions which need to get tight and close together

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15
Q

What is cysteine commonly found in?

A

Proteases

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16
Q

What do phenylalanine and tryptophan have?

A

Aromatic side chains (resonance structures)

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17
Q

What does the R group in proline do?

A

Bends back to the main chain N forming a 5 membered covalently closed ring. This makes it rigid.

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18
Q

What side chain do negatively charged polar (acidic) amino acids have?

A

One containing an acidic carboxyl group

19
Q

What side chain do positively charged polar (basic) amino acids have?

A

One containing a basic amine group

20
Q

What are common in non-polar side chains?

A

Have either C or H groups at end of side chain.

21
Q

What are common in polar side chains?

A

Have either -OH, -NH2, or -O at the end of their side chains.

22
Q

Non-polar amino acids are?

A

Hydrophobic

23
Q

Polar amino acids are?

A

Hydrophilic

24
Q

What are the three types of polar amino acids?

A

Uncharged, Positively charged, Negatively charged

25
Q

What is the pKa value?

A

pH at which the ionisable group is 50% ionised.

26
Q

What is the pI or Isoelectric point?

A

pH at which the net charge on an amino acid is zero

27
Q

The smaller the pKa…

A

the stronger the acid

28
Q

For non-ionisable amino acids the pKa is the ____ as the pI

A

Same

29
Q

pH < pKa = ?

A

Protonation (extra H atom)

30
Q

pH > pKa = ?

A

Deprotonation (is missing an H atom)

31
Q

Where is the RNA translated into proteins

A

ribosomes

32
Q

What is post translational modification?

A

Modification of amino acids after they are added to a protein.

33
Q

Cysteine can sometimes form a covalent bond with another nearby cysteine via?

A

Disulfide bonds.

34
Q

What are the main amino acid modification methods?

A

Phosphorylation,
Hydroxylation,
Carboxylation
Metal binding,
Iodination,
Glycosylation.

35
Q

Peptide cleavage:

A

Shortening of a peptide to ensure correct folding

36
Q

Cysteine - Cysteine disulfide bond formation allows?

A

Stability of protein structure

37
Q

Phosphorylation is…

A

addition of a phosphate, often acts as a switch, turning a protein on or off.

38
Q

Glycosylation is…

A

addition of glucose/sugars, increases stability and reduces flexibility of proteins

39
Q

Hydroxylation is…

A

addition of a hydroxyl group, converts hydrophobic residues into hydrophilic residues

40
Q

Carboxylation is…

A

addition of a carboxyl group, mostly occurs in blood clotting proteins

41
Q

What is the name of the covalent bond in joining amino acids?

A

Peptide bond

42
Q

What are the characteristic of the peptide bond

A

Planar, Trans, Dipole.

40% double bond character leads to planairty, rotational barrier of -80KJ/mol.

43
Q

What are amino acid residues?

A

amino acids that are covalently bonded, leading to them being no longer complete, individual amino acids.

BIOC192 2024 (35 decks)

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