3.3.13 Amino acids, proteins and DNA

Question 1

What is an amino acid?

Answer 1

• An amino acid has a basic amino group (NH₂ and an acidic carboxyl group (COOH). This make them amphoteric.
• They’re chiral molecules because the carbon has four different groups attached. So a solution of a single amino acid will rotate plane polarised light
• They have an R group which is an organic side chain - (glycine is an exception as the R group is just an H)

Question 2

What is amphoteric?

Answer 2

When a molecule has both acidic and basic properties

Question 3

What is the common name of an amino acid

Answer 3

E.g. glycine/ valine

Question 4

How do you name proteins using their systematic name, use alanine as an example?

Answer 4

1. Find the longest protien chain that includes the carboxylic acid group and write down its name - e.g. for alanine the longest C chain containing a COOH group is 3C long… propanoic acid
2. Number the carbons in the chain starting with the carbon in the carboxylic acid group as No. 1
3. Write down the positions of any NH₂ groups and show that they are NH₂ groups with the word “amino” - e.g. alanine has a NH₂ group on carbon-2
4. Include any other functional groups when naming the molecule

Therefore the systematic name for alanine is 2-aminopropanoic acid

Question 5

What is a zwitterion?

Answer 5

A dipolar molecule - it has both a postive and negative charge in different part of the molecule

Question 6

Explain how amino acids can be zwitterions

Answer 6

Zwitterions only exist near an amino acids isoelectric point. This is the pH where the average overall charge on the amino acid is zero. It’s different for different amino acids depending on their R-group

Isoelectric point - both the carbonyl group and the amino group are likely to be ionised:

H₃N⁺CRHCOO^-

Question 7

Give the structure of an amino acid in conditions more acidic than it’s isoelectric point

Answer 7

At low pH the COO^- group is more likely to gain an H⁺

H₃N⁺CRHCOOH

Question 8

Give the structure of an amino acid in conditions more alakaline than its isoelectric point

Answer 8

At high pH the NH³ group is likely to lose an H⁺

H₂NCRHCOO^-

Question 9

Why can amino acids be identified using thin-layer chromatography?

Answer 9

Amino acids have different R groups, so they will have different solubilities in the same solvent. This means that you can easily separate and identify all of the different amino acids in a mixture using

Question 10

Give the method of thin layer chromatography for proteins

Answer 10

1 - Draw a pencil line near the bottom of a thin layer chromatography plate and put a concentrated spot of the mixture of amino acids on it
2 - Dip the bottom of the plate (not the spot) into a solvent
3 - As the solvent spreads up the plate, the different amino acids move with it, but at different rates, so they separate out
4 - When the solvent’s nearly reached the top, take the plate out and mark the solvent front with a pencil. Then leave the plate to dry
5 - Amino acids aren’t coloured so they need to be amde visible by:
~ being sprayed with ninhydrin solution on the plate, turning the spots purple
~ by using a special plate with a fluorescent dye added to it. The dye will glow when UV light is shined on it, the spots of chemical (protein) will cover the plate making it appear dark, the spots can then be drawn around to show where they are without UV
6 - The R_f vaule can be calculated, and compared to a table of know R_f values to identify the amino acids

Question 11

Give the equation to work out R_f value

Answer 11

R_f = x/y = distance travelled by spot/distance travelled by solvent

Question 12

Explain how proteins are condensation polymers of amino acids

Answer 12

Proteins are made up of lots of amino acids joined together by peptide links. The chain is put together by condensation reactions and broken apart by hydrolysis reactions

Proteins are really polyamides

Question 13

What is the amide link called in a protein?

Answer 13

Peptide link/bond

Question 14

Give the equation for when two amino acids join to make a dipeptide

Answer 14

H₂NCRHCOOH + H₂NCR’HCOOH <=> H₂NCRHCONHCR’HCOOH + H₂O

Question 15

Explain how a dipeptide can be used to continue the chain

Answer 15

The dipeptide still has a NH₂ group at one end and a COOH group at the other end, so can react in other condensation reactions with other amino acids to produce a polypeptide chain

Question 16

Give the conditions required to hydrolyse a protein into it’s amino acid monomers

Answer 16

Add hot aqueous 6 M hydrochloric acid and heat the mixture under reflux for 24 hours

Question 17

How can you work out which amino acids are in a protein chain?

Answer 17

Break each of the peptide links down the middle, then add either an H atom or an OH group to each of the broken ends to produce the original amino acids monomers

Question 18

What are the four levels of protien structure?

Answer 18

1. Primary
2. Secondary
3. Tertiary
4. Quarternary - not required

Question 19

Describe a primary protein structure

Answer 19

The primary structure is the sequence of the amino acids in the long chain that makes up the protien (the poly peptide chain)

Question 20

Describe a secondary protein structure

Answer 20

The peptide links can form hydrogen bonds with each other, meaning the chain isn’t a straight line. The shape of the protien is called it’s secondary structure. The most common secondary structure is a spiral called an alpha (α) helix. Another common type is a beta (β) pleated sheet. This is a layer of protein folded like a concertina

Question 21

Describe a teritiary protien structure

Answer 21

The chain of amino acids is itself often coiled and folded in a charecteristic way that identifies the protien. Extra bonds can form between different parts of the polypeptide chain, which give the protein a three dimensional shape. This is it’s tertairy structure.

Question 22

What are the two types of bond that hold proteins in shape

Answer 22

• Hydrogen bonding
• Disulfide bond

Question 23

Why is it important that a protein holds it’s shape using intermolecular forces and bonding?

Answer 23

This effect the secondary and teritiary structure which effect how the protein folds or twists, this effects shape. The shape of the protein is vital to how it function - e.g. changing a shape of an enzyme may denature it

Question 24

How does hydrogen bonding effect the shape of the protien?

Answer 24

Hydrogens bonds exist between polar groups - e.g. -OH and -NH₂. They stabalise both the secondary and tertiary structure of the protein

Question 25

How do disulfide bonds effect the shape of the protien?

Answer 25

The amino acid group cystine contains a thiol group (-SH). Thiol groups on different cystine residues can lose their H atoms and join together forming a disulfide bond. These disulfide bonds link together different parts of the protein chain and help to stabalise the tertiary structure

Question 26

What factors effect the shape of a protien?

Answer 26

Temperature an pH can affect hydrogen bonding and the formation of disulfide bridges and so can change the shape of the protein

Question 27

What are enzymes?

Answer 27

Enzmes are proteins that acts as biological catalysts speeding up chemical reactions

1. They catalyse every metabolic reaction in the bodies of living organisms
2. Enzymes are protiens. Some have non-protein components
3. Every enzyme has an area called an active site. This is the part of the enzyme where the substrate fits into so that it can interact with the enzyme
4. The active site is three-dimensional - it’s part of the tertiary structure of the enzyme protein

Question 28

Explain the lock and key model

Answer 28

• Enzymes only work with specific substrates, typically only one
• For an enzyme to work the substrate must fit the acitve site, if it doesn’t fit then the reaction won’t be catalysed. This is called the lock and key model
• Enzymes are unchanged by the reaction as they are catalysts
• Enzymes are made up of amino acids so they have chiral centres - this makes their acitve sites stereospecific - they will only work with one enantiomer of a substance, the other enantionmer won’t fit the active site

Question 29

What are inhibitors?

Answer 29

• Molecules that have a similar shape to the substrate act as enzyme inhibitors
• They compete with the substrate to bond to the active site, but no reaction will follow. Instead they block the active site, so the subtrate cannot fit

Question 30

What effects the amount an enzyme is inhibited?

Answer 30

Depends on the relative concentrations of the inhibitor and substrate - if there’s more of the inhibitor, it’ll take up more of the active sites and very little substrate will be able to get to the enzyme

The amount of inhibition also depends on how strongly the inhibitor bonds to the active site

Question 31

Explain how drugs can act as inhibitors

Answer 31

Some drugs are inhibitors that block the active site of an enzyme and stop it from working - e.g. some anitbiotics work by blocking the active site of an enzyme in bacteria that helps to make their cell walls, causing thier cells walls to weaken overtime and causing the cell to eventually burst

Question 32

Why can it be challenging to make drugs that inhibit enzymes?

Answer 32

The acitve site of an enzyme is very specific, so it takes lots of effort to find a drug molecule that will fit into the active site. Especially when a drug molecule is chiral as only one enantiomer will fit into the acitve site, because the active sites of enzymes are stereospecific

Question 33

How are drugs that inhibit enzymes usually dicovers?

Answer 33

Drugs are often found by trial and error. Scientists carry out experiments using lots of compounds to see if they work as inhibitors for a particular enzyme. They’ll then adapt any that work to see if they can improve them. This process takes a long time.

Question 34

How can the discovery of drugs that inhibit enzymes be sped up?

Answer 34

By using computers to model the shape of an enzymes active site and predict how well potential drugs will interact with it. They can quickly examine hundreds of molecules to look for ones that might be the right shape before the start synthesising drugs in the lab.

Question 35

What is DNA?

Answer 35

DNA or Deoxyribonucleic acid contains all the genetic information of an organism.

DNA is a polymer made of many monomers called nucleotides. The nucleotides join together to form a polynucleotide chain. Covalent bonds form between the phosphate group of one nucleotide and the suger of another - this makes a the suger-phosphate backbone of the chain

Question 36

What are nucleotides made from

Answer 36

1. A phosphate group
2. A pentose suger - a 5C sugar, In DNA the sugar is 2-deoxyribose
3. A base - one of four different bases

Question 37

What are the four base in DNA

Answer 37

1. Adenine
2. Guanine
3. Cytosine
4. Thymine

Question 38

Explain how DNA is formed by condensation polymerisation

Answer 38

A water molecule is lost and a phosphodiester bond is formed between the OH groups on the sugar and the phosphate
There are still OH groups at the top and bottom of the chain, so further links can be made. This allows nucleotides to form a polymer made up of an alternating sugar phosphate-sugar-phosphate chain.

Question 39

What structure does DNA take

Answer 39

• A double helix, made form two polynucleotide strands
• The strands are held together by hydrogen bonds between bases

Question 40

Explain complementary base pairing

Answer 40

Each base can only bond with another complemetary base, the two strands of DNA are therefore complementary to eachother e.g. adenine on one strand will always be opposite thymine

Question 41

Why do adenine and thymine bond together, but not to cytosine and guanine

Answer 41

Due to the arrangement of their atoms, two hydrogen bonds can be formed between the δ+ H atoms and a lone pair on the opposite O or N atom.

To bond atoms must be the right distance apart

Question 42

Why do cytosine and guanine bond together, but not to adenine and thymine

Answer 42

Due to the arrangement of their atoms, three hydrogen bonds can be formed between the δ+ H atoms and a lone pair on the opposite O or N atom.

Question 43

Why are A+T and C+G the only case pairings

Answer 43

They are the only possible base combinations. Other base pairing would put partially charged atoms to close together (causing repulsion), or too far apart, or the bonding atoms wouldn’t line up properly.

The DNA helix is twisted for a similar reason so the bases are in the right alignment and at the right distance apart for complementary bases to form.

Question 44

What is cisplatin?

Answer 44

Cisplatin is a complex of platinum(II) with two chloride ion ligands and two ammonia ligands in a square planar shape. It’s used as an anti-cancer drug.

The two chlorine ions are next to each other so the complex is cisplatin, if they were opposite it would be transplatin, which has different biological effects

Question 45

How does cisplatin prevent cancer?

Answer 45

• Cancer is caused by cells dividing uncontrollably and forming tumours
• In order to divide a cell has to replicate it’s DNA
• Cisplatin binds to DNA causing kinks in the DNA helix which stop the proteins that replicate the DNA from copying it properly. This stops the tumour cells from reproducing

Question 46

How does cisplatin create kink in the DNA?

Answer 46

• A nitrogen atom on a guanine base in DNA forms a co-ordinate bond with cisplatin’s platininum ion, replacing one of the chloride ion ligands
• A second nitrogen atom from a nearby guanine (either on the same strand of DNA or the opposite strand) can bond to the platinum and replace the second chloride ion
• The presense of the cisplatin ion complex bound to the DNA strands causes the strands to kink, meaning DNA strands can unwind to be copied properly - so the cell can’t replicate

Damage to the DNA triggers mechanisim that cause the cell to die

Question 47

What are the disadvantages of cisplatin?

Answer 47

Cisplatin can bind to DNA in healthy normal cells as well as cancer cells. This is particularly a problem for cells that replicate frequently, such as hair and blood cells, because cisplatin stops them from replicating in the same way it does to cancer cells. This means that cisplatin can cause hair loss and supress the immune system (which is controlled by white blood cells). It can also cause kidney damage.

Question 48

How can the side effect of cisplatin be reduced?

Answer 48

• Lowering the dossage of cisplatin given to the patient
• Targeting the tumour/ administering locally - this means using a method that deliver the drug only to the cancer cells, so it doesn’t get a chance to attack healthy cells

Question 49

Why is cisplatin still used as a chemotherapy drug despite the side effects?

Answer 49

Because the balence of the long-term positves effects (curing cancer) outweigh the negative short-term effects