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PHS2102 > Lecture 6: proteins > Flashcards

Lecture 6: proteins Flashcards

1
Q

What are the two types of isomers in amino acids?

A
  1. L isomer: left handed turn
  2. D isomer: right handed turn
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2
Q

All amino acids in proteins are _____isomers?

A

L

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3
Q

What is the isoelectric point?

A

The pH at which the amino acid carries a net charge of zero

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4
Q

How do you calculate the isoelectric point (pI)?

A
  1. If the amino acid does not have an ionisable R group:
    pI = the average of the pKa of the amino and carboxylic group
  2. If the amino acid has an ionisable R group:
    - locate the pKa for which the amino acid has a net charge of +1 and -1
    - Take the average of the 2 pKa values
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5
Q

What are the 4 classifications of amino acids?

A
  1. Non polar aliphatic
  2. Aromatic
  3. Uncharged polar
  4. Charged polar
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6
Q

Which type of amino acid has a UV absorbing property?

A

Aromatic

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7
Q

What are the intermolecular forces that can be formed between R groups of amino acids?

A
  1. Hydrogen bonds
  2. Hydrophobic interactions
  3. Disulfide bonds
  4. Ionic bonds
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8
Q

Which proteogenic amino acid is not coded by standard codons but can be incorporated into the polypeptide though a stop codon?

A

Selenocysteine
(stop codon: UGA)

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9
Q

What makes amino acids non-proteogenic?

A

There is no codon coding for them

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10
Q

A polypeptide made up of ____ or more amino acids is called a protein.

A

50

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11
Q

What are the types of secondary structures?

A
  1. Alpha helix
  2. Beta sheet
  3. Beta turn
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12
Q

What is the pattern of intermolecular forces found in alpha helixes?

A

Hydrogen bonding between carbonyl group of an amino acid and amino group of an amino acid 4 residues away from it.

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13
Q

Is the alpha helix right or left handed?

A

right

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14
Q

Which amino acids tend to not form alpha helixes and why?

A
  1. Glycine: it is too flexible, alpha helix needs rigidity
  2. Proline: structure too short, alpha helix will break
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15
Q

How are hydrogen bonds formed in the beta sheet?

A

Formed across adjacent segments of the polypeptide chain, in right angles to the direction of the polypeptide strands

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16
Q

What is a beta turn?

A

It is a segment of the polypetide forming a beta sheet that abruptly reverses the direction

17
Q

How many amino acids is a beta turn made out of?

A

4

18
Q

Where does protein folding most commonly occur in mammalian cells?

A

Endoplasmic reticulum

19
Q

What are factors that cause protein unfolding?

A
  1. pH changes
  2. High temperatures
  3. Organic solvents
  4. Denaturing agents
20
Q

What are the types of post translational modifications to proteins?

A
  1. Phosphorylation
  2. Carboxylation
  3. Glycosylation
    4.Conjugation with lipids
  4. Hydroxylation
  5. Oxidation
  6. Hydrolysis
21
Q

Which amino acid is subjected to carboxylation?

A

glutamate

22
Q

Where does N linked glycosylation occur, and which residues are glycosylated?

A
  1. RER and Golgi apparatus
  2. N atom in side chain of asparagine residues
23
Q

Where does O linked glycosylation occur, and which residues are glycosylated?

A
  1. Golgi apparatus
  2. O atom in side chains of Serine and Threonine residues
24
Q

How are lipids conjugated to proteins?

A

Polar group of the lipid is attached to:
1. N terminal
2. Cysteine reside through a thioester linkage

25
Q

On which amino acid does hydroxylation occur?

A

Proline

26
Q

On which amino acid does oxidation occur and why is it important?

A
  1. Cysteine
  2. Important as it allows for the formation of the disulfide bond between 2 cysteine residues.
27
Q

What is the function of hydrolysis?

A
  1. Convert pro-active proteins into active form by removal of a certain peptide fragment
  2. Degrade proteins into amino acids/peptides
28
Q

What kind of amino acids can be phosphorylated?

A

Serine, threorine and tyrosine
because they have hydroxyl groups

29
Q

What are the aromatic amino acids?

A

tyrosine, phenylalanine, typtophan

30
Q

What are the aliphatic non polar amino acids?

A

glycine, valine, alanine, leucine, isoleucine

31
Q

What are the hydroxyl containing aliphatic amino acids?

A

serine, threorine

32
Q

What are the acidic amino acids?

A

aspartic acid, glutamic acid

33
Q

What are the basic amino acids?

A

arginine, lysine, histidine

34
Q

What are the amino acids containing amide groups?

A

asparagine, glutamine

35
Q

What are the sulfur containing amino acids?

A

methionine, cysteine

PHS2102 (15 decks)

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