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Chemistry Year 13 > Amino Acids, Proteins And DNA > Flashcards

Amino Acids, Proteins And DNA Flashcards

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1
Q

What is the structure of an amino acid?

A

They are bifunctional molecules. They contain an amino functional group (-NH2) and a carboxylic acid (-COOH) functional group. They also have a side chain group (an R group)

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2
Q

What is an a-amino acid/ 2-amino acid?

A

Where the amino group is bonded to the carbon atom adjacent to the carboxylic acid group

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3
Q

Why apart from glycine are all a-amino acids optical isomers?

A

Because the central carbon atom in these amino acids is bonded to four different groups

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4
Q

Why can an amino acid act both as a weak acid and a weak base?

A

Because the -COOH group is weakly acidic and tend to donate its proton to water, while the -NH2 group is weakly basic and tends to accept a proton from water via the nitrogen lone pair

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5
Q

What is a zwitterion of an amino acid?

A

When in a pH that is not tok highly acidic or alkaline the amino acid acts simultaneously as both an anion and a cation

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6
Q

What is an amino acids isoelectric pH?

A

The unique value that the zwitterion of each amino acid exists at in solution

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7
Q

Apart from in solution where else do zwitterions exist?

A

In the crystalline form of the amino acid

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8
Q

Why do amino acids have relatively high melting and boiling points?

A

Because of the electrostatic attraction between the oppositely charged parts of the ion

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9
Q

What type of molecule is a protein?

A

A condensation polymer of amino acids

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10
Q

How is a dipeptide bond formed?

A

The -NH2 group of one amino acid can undergo a condensation reaction with the -COOH group of another amino acid eleminating a water molecule

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11
Q

What is the amide group (-CONH-) that links the two amino acids called and what is the C-N bond within this group called?

A

The amide group is called a peptide link and the C-N bond within the group is called the peptide bond

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12
Q

What is the end of the dipeptide with the amino group called?

A

The amino terminus

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13
Q

What is the end of the dipeptide with the carboxylic acid called?

A

The carboxyl terminus

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14
Q

How can the structures of peptides be written using abreviations using glycine and alanine as an example?

A

E.g. HOOC -Gly - Ala - NH2

This shows that the glycine is bonded to the alanine via its amine leaving the carboxylic acid free and the alanine is bonded to the glycine via its acid leaving its amine group free

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15
Q

What is the primary structure of a protein?

A

The order of amini acids in the chain of the protein

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16
Q

What are the two secondary structures of a protein?

A

a-helix and B -pleated sheet

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17
Q

How is an a-helix structure formed and what is this structure?

A

Hydrogen bonds can form between an N-H group from one peptide link and a C=O group from another peptide link four amino acids further doen the protein chain to form an a-helix. The helical shape is held in place by a regular pattern of hydrogen bonds. All the R groups attached to the protein are attached to the outside of the helix. The helic is elastic and flexible

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18
Q

How is the B-pleated sheet structure formed and what is this structure?

A

Two or more parallel regions of the protein can line up so that hydrogen bonds form between an N-H group from one peptide link and a C=O group from another peptide link much further up the chain in another parallel region. Many parallel strands can interact side by side leading to a flat sheet like structure

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19
Q

What is the overall 3D shape of the whole protein called?

A

Its tertiary structure

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20
Q

How is the folding of the different regions of the secondary structure to build it’s tertiary structure determined?

A

By the various electrostatic or covalent links between the R side chainw or amino acid residues in the protein

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21
Q

What bond can be formed to help determine the tertiary structure if the protein contains cysteine amino acids?

A

The side chain -SH groups can react together to form a strong S-S disilfide bridge (cysteine link). This is a covalent bond

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22
Q

When can the S-S bond be broken and what does this cause?

A

The S-S bond can be broken if the protein is heated, reduced or treated with base and this can cause the collapse of the biologically acrive tertiary structure

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23
Q

What does it mean when a protein is denatured?

A

The tertiary structure has broken down and the protein is no longer biologically active

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24
Q

Apart from cysteine links what else contributes to the overall tertiary structure of a protein?

A

Ionic interactions and hydrogen-bonding interactions between R groups of the side chains of amino acids

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25
Q

Why are many proteins biologically active over a very narrow pH range?

A

Because if the pH is changed the interactions (e.g. ionic and hydrogen) between different side chains could be broken

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26
Q

How can the amino acids be counted and identified?

A

Using thin-layer chromatography

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27
Q

How does thin-layer chromatography take place in regard to amino acids?

A
  • a small spot of mixture is added near to the bottom of a TLC plate and the plate is dipped in a solvent making sure the spot is above the solvent line
  • As the solvent moves up the TLC plate different amino acids move up at different rates
  • the TLC plate is removed when the solvent has nearly reached the top of the plate and the compounds are revealed using an appropriate technique
  • the most common approach to revealing the amino acids is to spray the solution with an ethanol solution of ninhydrin. Ninhydrin reacts with the amine groups of the amino acids and produces a blue-purple colour.
  • once the amino acids have been visualised, a retention factor (Rf) can be calculated for each amino acid and used to identify the amino acid composition of the protein by comparisom with known data
28
Q

How are proteins broken down?

A
  • in our bodies through digestion
  • in the lab we can hear them with 5 mol dm-3 hydrochloric acid for about 24 hours. The secondary and tertiary structures are rapidly broken down causing the polyamide chain to unravel. The chain is then hydrolysed at each of the peptide links and liberates the component amino acids
29
Q

What are enzymes?

A

Proteins that catalyse specific chemical reactions often by a factor of 106-1012 times. Enzymes catalyse biological reactions under the conditions found in living cells

30
Q

What are enzymes?

A

Proteins that catalyse specific chemical reactions often by a factor of 106-1012 times. Enzymes catalyse biological reactions under the conditions found in living cells

31
Q

Why does it mean that enzymes show great specifity?

A

They will only catalyse specific reactions/ reaction

32
Q

What is the reactant in an enzyme-catalysed reaction called?

A

The substrate

33
Q

Where does the reaction of the substrate take place in the enzyme and what is this?

A

The active site. The active site is normally a cleft or hole in the protein in which the substrate can fit

34
Q

What is the enzyme-substrate complex and what happens in it?

A

This is produced when the substrate enters the active site. The substrate is said to be bound to the active site. The enzyme then catalyses the reaction of the substrate to give the product and ejects the product from the active site

35
Q

What is the structure that gives an enzyme it’s active site?

A

It’s 3D tertiary structure

36
Q

What is the lock and key hypothesis?

A

That only molecules that have the right shape can fit into the active site

37
Q

Why do the side chains in the amino acids that make up the enzyme play an important role in the attraction and bonding of the substrate to the enzyme?

A
  • the side chains may contain -OH groups that can hydrogen bond to the substrate, or ionic groups such as the -NH3+ or -COO- which can attract the substrate by electrostatic forces.
  • Amino acids that contain hydrocarbon side chains can also contribute to bonding of the substrate by van der waal forces
  • the substrate must have the correct functional groups displayed in the correct orientation in space to be capable of interacting with the side chains of the active site efficiently
38
Q

Why are amino acids chiral?

A

Because they are made from l-amino acids.

39
Q

What is a Stereospecfiic active site?

A

An active site that will only bind to one enantiomer of a racemate.

40
Q

What is an enzyme inhibitor?

A

A molecule that binds to an enzymes active site and decreases its activity

41
Q

Why are many drugs that treat disease enzyme inhibitors and how do they do this?

A
  • if the activity of an enzyme in an organism such as a bacterium can be decreased then the organism may die
  • if a disease is caused by an imbalance in enzyme activity then an enzyme inhibitor might restore balance
  • many drugs act as enzyme inhibitors by blocking the active site of the enzyme
42
Q

In order for an inhibitor to be active what must it do?

A

Bind more strongly to the active site than the natural substrate does

43
Q

To design a drug which acts as an enzyme inhibitor we must know the 3D structure as well as the amino acid side chains present in the active site. How can we preduct the shape of enzymes and drugs?

A

By using sophisticated computer programmes

44
Q

What is deoxyribonucleic acid? (DNA)

A

An organic polymer that records genetic information

45
Q

What is DNA made up of?

A

Two polymer strands held together by H-bonding . It has a double helical shape. The monomers that make up DNA are called nucleotides.

46
Q

What does each nucleotide consist of?

A

Three components linked together, a phosphate, a sugar and a base

47
Q

What is the sugar in DNA?

A

2-deoxyribose, a modified version of the sugar ribose (used in RNA) missing a hydroxyl group at the 2 position

48
Q

How is 2-deoxyribose numbered?

A

Check snap camera roll

49
Q

In a nucleotide which numbers are the phosphate group and the base group attached to?

A

The phosphate group is attached to the 5 position of 2-deoxyribose and the base is attached to the 1 position

50
Q

What are the four bases that can be bonded to 2-deoxyribose?

A

Thymine, cytosine, adenine and guanine (T, C, A and G)

51
Q

What is the nucleotide containung the base adenine called? What type of acid is the phosphate and what is it at pH 7?

A

2-deoxyadenosine 5-monophosphate . The phosphate us a diprotic acid and at pH 7 is fully ionised

52
Q

What is the structure of a polynucleotide?

A

It has a backbone of sugars and phosphates and has the various bases attached to the backbone

53
Q

How is the polymer DNA made up?

A

By the linking of nucleotides via the phosphaye at the 5 position of one nucleotide and the hydroxyl group at the 3 position of a different nucleotide

54
Q

What is the double helix shape of DNA the result of?

A

Hydrogen bonding between bases in one polynucleotide strand and bases in a second strand (the complementary strand)

55
Q

What is the base pair bonding in DNA and why does this occur?

A

Adenine only bonds (H-bonds) with thymine and guanine only bonds with cytosine. This happens because these base pairs fit exactly in terms of size and shape, forming strong H-bond interactions

56
Q

How many bonds does the AT base pair make and how many does the GC base pair make?

A

The AT pair makes two H-bonds and the GC base pair makes 3 H-bonds

57
Q

How can a single polynucleotide strand of DNA be represented?

A

By writing the order of the bases starting at the end that contains the free 5 carbon and ending with the end that contains the 3 position. The complementary strand that makes the double helix runs in the opposite direction

58
Q

When a cell divides a new copy of it’s DNA must be made. How does DNA replicate itself?

A

By unwinding the double helix (this is catalysed by an enzyme). Next complementary nucleotides can bind to two unwound chains, ultimarely leading to two copies of the original DNA molecule

59
Q

Who were the main people that had an important role in DNA work?

A

James Watson, Francis Crick, Maurice Wilkins and Dr Rosalind Franklin

60
Q

What is the use of drugs to treat cancer called?

A

Chemotherapy

61
Q

How to many drugs that treat cancer work, why does this cause side effects and what are these side effects?

A
  • Many work by targetting cells that divide rapidly. These drugs may affect cell division by binding to DNA and stop replication.
  • They often cause side effects because other cells such as those that make up the gastrointestinal tract, hair follicles, and bone marrow also replicate quickly.
  • So many anticancer drugs have side effects such as nausea, hair loss and susceptibility to infection
62
Q

What us cisplatin?

A

An anticancer drug that is used to treat a number of different cancers.

63
Q

Does the isomer of cisplatin, transplatin show anticancer activity?

A

No

64
Q

What happens when cisplatin enters a cell?

A

One of the chlorides is initially replaced by water and then by one of the nitrogen atoms of a guanine base in DNA. This forms a nitrogen-platinum bond and fixes the drug to one strand of the DNA double helix. The second chloride is then lost from the platinum atom in the same way and this allows the guanine base to bind. This distorts the shape of DNA and prevents replication

65
Q

Why are chemotherapy doses given in small quantities?

A

To minimise damage to healthy cells, to allow the body to recover

Chemistry Year 13 (16 decks)

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