amino acids, proteins and DNA

Question 1

what is the general structure of an amino acid

Answer 1

NH2-CH-COOH with a R group attached to it

the R group can be a variety of different things depending on what amino acid it is

the NH2 and the COOH group are attached to the same C group

Question 2

what is the simplest amino acid

Answer 2

the simplest amino acid group is glycine where the R group is H

NH2- CH2-COOH

Question 3

describe the optical activity of amino acid

Answer 3

all amino acids exept glycine are chiral because there are four different groups around the C

they rotate plane polarised light

Question 4

how do you name amino acids

Answer 4

amino is often the lower priority group and therefore you use the prefix amino

you then use the suffix of the higher priority group
e.g.
NH2 - CH2 - COOH

2-aminoethanoic acid

Question 5

what are acid or basic amino acids

Answer 5

some amino acids have an extra carboxylic acid or an amine group on the R group.

These amino acids are classed as acidic or basic amino acids

e.g. 2,6-diaminohexanoic acid

Question 6

what are Zwitterions

Answer 6

The no charge form of an amino acid never occurs

The amino acid exits as a dipolar Zwitterion

Question 7

what is the state of an amino acid

Answer 7

amino acids are often acids

Question 8

why do amino acids have high melting points

Answer 8

The ionic interaction between zwitterions explains the relatively high melting points of amino acids opposed to the weaker hydrogen bonding that would occur in the in the no charge form

Question 9

describe the ph of amino acids in certain solutions

Answer 9

the amino group is basic and the carboxylic acid group is acidic

species in alkaline solution high ph:
- the amino acid loses a H+ from COOH

species in neutral solutions:
-forms the Zwitterion of amino acids

species in acidic solution low ph
-the amino group in the amino acid gains a H+ forming NH3

Therefore amino acids can act as weak buffers and will gradually change pH if small amounts of acid or alkalis are added to the amino acids

The extra carboxylix acid or amino amine group on the R group will also react and change form in alkaline and acid conditions

Question 10

what is an equation for an amino acid in a strong acid (low ph)

Answer 10

+NH2CH2COO- + HCL =CL-NH3+CH2COOH

Question 11

give an equation for an amino acid in a strong alkali (high ph)

Answer 11

+NH2CH2COO- + NaOH = NH2CH2CO2-Na+ + H2O

Question 12

what are dipeptides

Answer 12

dipeptides are simple combination molecules of two amino acids with one amide (peptide) link

for any two different amino acids, there are two possible combinations of the amino acids in the dipeptide

Question 13

what are the other reactions of amino acids

Answer 13

the carboxylic acid group and amine group in amino acids can undergo the usual reactions of these functional groups

e.g. esterfication reactions

Question 14

how do you hydrolyse dipeptides/ proteins

Answer 14

add aqueous concentrated hydrochloric acid and then heat the mixture under reflux for 24 hours

The composition of the protein molecule may then be deduced by using TLC chromatography

Question 15

describe thin-layer chromatography

Answer 15

1) wearing gloves, draw a pencil 1 cm above the bottom of a TLC plate and mark spots for each sample equally spaced along a line
2) use a capillary tube ti add a tiny drop of each solution to different spot and allow the plate to air dry
3) add a solvent to a chamber or large beaker with a lid so that it is no more than 1cm in depth
4) place the TLC plate into the chamber, making sure that the level of the solvent is below the pencil line. Replace the lid to get a tight seal
5. when the level of the solvent reaches about 1 cm from the top of the plate, remove the plate and mark the solvent level with a pencil. Allow the plate to dry in the fume cupboard
6. spray paper with ningydrin and put in oven - draw around them lightly in pencil
7. calculate the Rf values of the observed spots

Question 16

what is the Rf value

Answer 16

distance moved by the amino acid/ distance moved by the solvent

measure how far each spot travels relative to the solvent front and calculate the Rf value

Each amino acid has its own Rf value

compare Rd values to those known substances

Question 17

why do some substances don’t separate

Answer 17

some substances won’t separate because similar compounds have similar Rf values

So some spots may contain more than one compound

Question 18

why must plastic gloves be worn

Answer 18

to prevent contamination from the hand to the plate

Question 19

why must a pencil line be drawn

Answer 19

so that it will not dissolve in the solvent

Question 20

why must tiny drops be used

Answer 20

too big a drop will cause different drops to merge

Question 21

why must the depth of the solvent be monitored

Answer 21

if the solvent is too deep it will dissolve the sample spots the sample spots form the plate

Question 22

why must a lid be used

Answer 22

ti prevent evaporation of the toxic solvent

Question 23

why must we wait for the solvent to rise to the top

Answer 23

so it will get more accurate results if the solvent is allowed to rise to near the top of the plate but the Rd value can ve calculated if the solvent does not reach the top of the plate

Question 24

why must we allow the solvent to dry in a fume cupbaord

Answer 24

the solvent is toxic

Question 25

why must ninhydrin be sprayed

Answer 25

if ninhydrin is sprayed on amino acid and then heated for 10 minutes then red to blue spots appear

This is done because amino acids are transparent and cannot be seen
We can also shine UV light to see the position of spots

Question 26

what is the primary structure of amino acids

Answer 26

the primary structure of proteins is the sequence of the 20 different naturally occurring amino acids joined together via a series of condensation reactions with peptide links (also known as the amide functional group)

Question 27

what is the secondary structure of a protein

Answer 27

the 3D arrangement of amino acids with the polypeptide chain in a - helix shape is held in place by hydrogen bonds between the H of N-H group and the O of the C=O of the FOURTH amino acid along the chain

The R groups on the amino acids are all points to the OUTSIDE of the helix

Question 28

what is the other form in which the secondary structure be

Answer 28

the secondary structure can also take the form of a B- pleated sheets

The protein chain folds into parallel strands side by side

The protein chain is held into the pleated shape by hydrogen bonds between the H of N-H group and the O of C=O of the amino acid much further along the chain in the parallel region (like cellulose)

Question 29

what is the tertiary structure of proteins

Answer 29

the tertiary structure is the folding of the secondary structure into more complex shapes
It is held in place by interactions between the R- side in more distant amino acids

These can be a variety of interactions including hydrogen bonding sulfur-sulfur bonds and ionic interactions

Question 30

how can hydrogen bonds be held in place in a tertiary structure

Answer 30

hydrogen bonding is one type of force that holds proteins in shape.
Hydrogen bonds only exist between polar groups such as -OH and -NH2

These groups contain electronegative atoms which induce a partial positive charge on the hydrogen atom

The hydrogen is attracted to lone pairs of electrons on adjacent polar bonds and a hydrogen bond is formed

Question 31

how can ionic bonds form in a tertiary structure

Answer 31

ionic interactions could form between acidic amino acids and basic amino acids

There is a transfer of a hydrogen ion from the -COOH to the NH2 forming a zwitterion

Question 32

how can disulfide bonds be formed

Answer 32

if two cysteine side chains end up near each other due to folding on the protein chain, they react to form a sulfur bridge which is a covalent bond

cysteine contains a thiol group and this thiol group lose its H atoms and join together to form a disulfide -S-S bond with another thiol group

These disulfide bonds link together different parts of the protein and help to stabilise the tertiary structure

the reaction would lead to have the amino acid residues (which is the amidno acids that make up a protein) + 2H+ + 2e-

Question 33

what are enzymes

Answer 33

enzymes are proteins

Question 34

what is the structure of the amino acid active site

Answer 34

The active site of an enzyme is usually a hollow in the globular protein structure into which a substrate molecule can bond to the amino acid side chains through a variety of interactions:

• hydrogen bonding
• Van der Waals forces
• Permanent dipole forces
• ionic interactions

Question 35

how strong must be the interactions in the active site

Answer 35

the interactions need be strong enough to hold the substrate for long enough for the enzyme catalysed reaction to occur, but weak enough for the product to be released

Question 36

what are the only molecules that can fit in the active site of an enzyme

Answer 36

only substrate molecules with the right shape and corrected positions of functional groups will fit and bind to the active-site

This is called the lock and key hypothesis

Question 37

what happens when the substrate is chiral

Answer 37

if the substrate is chiral then it is likely that only one enantiomer will fit in the enzyme and so only one isomer will be catalysed

The active site is therefore stereospecific

Question 38

how can we drugs as enzyme inhibitors

Answer 38

many drugs act as enzyme inhibitors by blocking the active site

The inhibitor will often bind to the active site so stopping the substrate from attaching to the enzyme

some inhibitors can also attach elsewhere on the enzyme but in doing so can change the shape of the active site which stops its effectiveness

Computers can be used to help change design such as drugs

Question 39

what are the key molecules in DNA

Answer 39

A phosphate ion

2- deosxyribose (a pentose sugar)

the 4 bases:
- adenine

• guanine
• thymine
• cytosine

Question 40

what are nucleotides

Answer 40

a nucleotide is made up from a phosphate ion bonded to 2 - deoxyribose which is in turn bonded to one of the four bases:

• adenine
• cytosine
• guanine
• thymine

Question 41

what is a sugar phosphate chain

Answer 41

a single strand of DNA (deoxyiribonucleic acid) is a polymer of nucleotides linked by covalent bonds between the phosphate group of one nucleotide and the 2- deoxyiribose of another nucleotide

This results in a sigar phosphate polymer chain with bases attatched to the sugars in the chain

Question 42

how does DNA exist

Answer 42

DNA exists as two complementary strands of the sugar-phosphate polymer chain arranged in the form of a double helix

Question 43

What does the term complementary base strands mean

Answer 43

complementary means the two strands must have sequences that match all A to T and C to G

there are hydrogen bonds between base pairs which lead to the two complementary strands of DNA

Guanine pairs wi

Question 44

what is cisplatin

Answer 44

cisplatin is used as an anticancer drug

The cisplatin version only woks as two chloride ions are displaced and the molecule ins on the DNA

In doing this, it stops the replication of cancerous cells

Cisplatin prevents DNA replication in cancer in cancer cells by a ligand replacement reaction with DNA in which a dative covalent bond to formed between platinum and a nitrogen atom on guanine

Question 45

what else can cisplatin do

Answer 45

cisplatin can also prevent the replication of healthy cells by bonding on to the healthy DNA which may lead to unwanted side effects like hair loss

Unwanted side effects can be minimised by giving cis-platin in small doses

Society needs to assess the balance between the benefits and the adverse effects of drugs such as the anticancer drug cisplatin