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Chemistry > 30 - Amino Acids, Proteins and DNA > Flashcards

30 - Amino Acids, Proteins and DNA Flashcards

1
Q

What are amino acids?

A

Made up of two functional groups, a carboxylic acid and a primary amine.

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2
Q

Are amino acids optically active?

A

Yes, due to the asymmetric carbon atom.
Almost all naturally occurring amino acids exist as (-) enantiomers.

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3
Q

What tendencies do the two functional groups on amino acids have?

A

Carboxylic acid group has a tendency to lose a proton.
Amine group has the tendency to accept a proton.

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4
Q

What is a zwitterion?

A

An ion with both permanent positive and negative charge, that is overall neutral.

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5
Q

What makes amino acids zwitterion?

A

Positive NH3+
Negative COO-

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6
Q

What is the melting point of amino acids like?

A

High melting points as they are ionic.

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7
Q

What is the solubility of amino acids like?

A

Dissolves well in water, due to their ionic nature and their ability to hydrogen bond.
Insoluble in non-polar solvents.

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8
Q

What does it mean if an amino acid is protonated?

A

Amino group has gained a hydrogen ion (NH3+).

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9
Q

What does it mean if an amino acid is deprotonated?

A

Carboxylic group has lost a hydrogen ion (COO-)

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10
Q

What do amino acids form when treated with acids or alkalis?

A

Salts

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11
Q

What are peptides?

A

Amino acids linked together by amide/peptide linkages, which form through a condensation reaction.

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12
Q

What is the cleavage point of peptides?

A

The OC-NH bond on the amide linkage.

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13
Q

Up to how many amino acids are peptides?

A

2-9

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14
Q

Up to how many amino acids are polypeptides?

A

10-50

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15
Q

Up to how many amino acids are proteins?

A

More than 50

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16
Q

How can peptides be broken down?

A

By hydrolysis, into their constituents amino acids.

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17
Q

What does hydrolysis of peptides with alkaline conditions produce?

A

NH2 becomes NH3+ (HCl -> NH3+Cl-)

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18
Q

What does hydrolysis of peptides with acidic conditions produce?

A

COOH becomes COO- (NaOH -> COO-Na+)

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19
Q

What are the advantages of alkaline/acidic conditions during hydrolysis of peptides?

A

Faster
Works at lower temperatures.

20
Q

How can amino acids be identified after hydrolysis of peptides?

A

Thin-Layer chromatography.

21
Q

What is the stationary phase in TLC?

A

Thin layer of silica on a thin, flexible, plastic sheet.

22
Q

What is the mobile phase in TLC?

A

Liquid solvent that moves through the stationary phase.

23
Q

What is the formula for Rf values?

A

Distance moves by solvent

24
Q

What should the value of Rf values be?

A

Less than one

25
Q

What determines the distance an amino acid moves during TLC?

A

Depends on its affinity for the mobile phase (solvent) vs the stationary phase, which depends on the intermolecular forces between the amino acid and the solvent.

26
Q

How are amino acids identified after TLC?

A

The plate is sprayed with a developing agent which makes the amino acids visible.
Then identified using Rf values.

27
Q

What is 2D TLC?

A

If the amino acid dots aren’t separated enough to be distinguished from one another the process of TLC is repeated with a different solvent.

28
Q

What are the three different ways amino acids bond in a protein chain?

A

Hydrogen bonding between C=O & N-H
Ionic attractions between COO- & NH3+
Sulfur-sulfur bonds (disulphide bridge)

29
Q

What is a sulfur-sulfur bond (disulphide bridge)?

A

Some amino acids have a R-SH group which will react with the amino group on another amino acid.

30
Q

What is a primary protein structure?

A

A linear sequence of amino acids held together by covalent bonding.

31
Q

How are primary protein structures represented?

A

By a sequence of three letter names of relevant the amino acids.

32
Q

What is a secondary protein structure?

A

A protein chain may form a helix (alpha helix), which is stabilized by hydrogen bonding between amide groups and C=O groups 4 units away OR it may form a beta-pleated sheet which is when polypetide chains line up in a parallel arrangement held together by hydrogen bonds between C=O and N-H.

33
Q

Compare the strength stability of primary and secondary protein structures?

A

Primary structures are relatively stable and requires harsh conditions to separate it.
Secondary structures are easily disrupted as hydrogen bonds are weaker than covalent bonds.

34
Q

What is a tertiary protein structure?

A

The alpha helix or beta pleated sheet coiled in a three-dimensional shape, held together by hydrogen bonding, ionic bonding and sulfur-sulfur bonds.

35
Q

What are enzymes?

A

Protein based catalysts

36
Q

What is the structure of enzymes?

A

Globular proteins with a crevice called an active site where reactions take place. Only molecules that fit the active site can react.

37
Q

How do enzymes catalyse a reaction?

A

The substrate bonds temporarily to the active site via intermolecular forces (enzyme-substrate complex). Whilst bonded the forces promote the moment of electrons within the substrate that lowers the activation energy.

38
Q

What are stereospecific enzymes?

A

Enzymes that will only catalyse the reaction of one enantiomer.

39
Q

What is a competitive inhibitor?

A

They have a structure similar to the substrate and competes with the substrate for the active site, preventing the binding of the substrate.

40
Q

When are competitive inhibitors use?

A

To stop harmful enzyme catalysed reactions in the body.

41
Q

What is a nucleotide?

A

Monomers which make up DNA. Complementary base pair with a sugar (deoxyribose) and a phosphate backbone.

42
Q

How do nucleotides combine?

A

Through condensation reactions.

43
Q

What bonds form between nucleotides?

A

Phosphodiester
Covalent bonds

44
Q

What are the phosphodiester bonds that forms between nucleotides?

A

The linkage between the 3rd carbon of one sugar molecule and the 5th carbon of another.

45
Q

Where do the covalent bonds form between nucleotides?

A

The phosphate group and two 5-carbon ring carbohydrates (pentoses) over two ester bonds.

46
Q

What happens to DNA during cell division?

A

A single strand of DNA acts as the template for the sequences of bases for the second strand. Separate nucleotides pair up with the bases, which form hydrogen bonds between one another. (Based on sterics) The product coils into a helix, held in place by hydrogen bonds.

47
Q

How can we disrupt DNA replication?

A

With cis-platin, which is a compound that has the perfect bond length to bond onto a A/G base pairs, preventing effective DNA replication.

Chemistry (24 decks)

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