Amino acids, proteins and DNA

Question 1

draw the structure of a- amino acids
name the 2 functional groups
how many naturally occurring amino acids
what amino acids are used for 
where they're found

Answer 1

NH2CH(R)COOH
amine and carboxylic acid group
20 naturally occurring
they’re the building bocks of proteins + found in muscles, organs enzymes and hormones

Question 2

describe the structure of amino acids

Answer 2

• amino acids are amphoteric, meaning they will undergo both acidic and basic reactions
• amino acids exist as zwitterions at neutral pH, as the carboxyl group behaves as an acid and loses a proton whilst the amine group behaves as a se and gains a proton.
• zwitterions are uncharged overall.

Question 3

define zwitterion

Answer 3

a dipolar ion containing both a positive and a negative charge

Question 4

what does the charge of the amino acid depend on? more pH? more OH-?

Answer 4

the charge of an amino acid is dependent on the pH
no charge= isoelectric point
(more H+, decreased pH= positive charge)
(more OH-, increased pH= negative charge)

Question 5

draw the equilibrium that the carbonyl group of amino acids exists in?
what happens if the conc of H+ increases?

Answer 5

-COOH ⇌ -COO- + H+
if the conc of H+ ions increases, the position of equilibrium will move to the left, increasing he conc of amino acids that exist with a -COOH group

Question 6

draw the equilibrium that the amine group of amino acids exists in?
what happens if the conc of OH- increases?

Answer 6

H+ + :NH2 ⇌ N+H3
if the conc of OH- increases, the OH- reacts with H+ ions, forming H20 and decreasing the conc of H+ ions
therefore, the position of equilibrium shifts left, increasing the conc of amino acids that exist with a neutral N+H3

Question 7

define proteins

Answer 7

condensation polymers of amino acids

Question 8

how are proteins hydrolysed?

Answer 8

by refluxing with every conc (6moldm-3) HCl for 24 hours

Question 9

how are amino acids separated and analysed?

Answer 9

using thin layer chromatography
1-differenet amino acids have different R groups, so they all have different affinities for the solvent
2- in thin-layer chromatography, each amino acid will move up the plate at a diff rate, depending on its affinity for a particular solvent
3-amino acids are colourless, so to make them visible a developing agent is used, such as ninhydrin or ultraviolet light

Question 10

how do you identify an amino acid? Calculate?

Answer 10

Rf value of amino acid= dx / dy = distance travelled by spot / distance travelled by solvent

1-measure the distance between the pint of origin and the middle of a spot
2-measure the distance moved by the solvent (solvent front) and the pint of origin
3- the Rf value can now be calculated using the above equation

Question 11

describe the structure of the 3 levels of protein structure

Answer 11

primary structure= sequence of amino acids in the polypeptide chain

• order of amino acids depends of protein being made
• its the most stable level of protein structure, as it is held together by strong covalent bonds

secondary structure= the ways the chains of amino acids interact with each other to form either an a-helix or a B-pleated sheet
-the peptide chains are hydrogen bonds

tertiary structure= the 3D into which the a-helix or B-pleated sheet is folded

Question 12

what leads to the secondary and tertiary structures? and what are these bonds affected by?

Answer 12

the intermolecular forces which are

• hydrogen bonds -stabilise both the 2ry and 3ry structures
• van der waals and dipole- dipole forces- stabilise 3ry structures
• disulphide bonds- they’re only important when the amino acids cysteine is part of the protein

-these bonds are affected by changes in pH and temperature, so any changes to these can change the shape of the protein

Question 13

what are enzymes and active sites and how do enzymes work?

Answer 13

enzymes are protein based biological catalysts meaning they increase the rate of biological reactions

• enzymes are globular proteins, though some enzymes also have non-protein components
• enzymes have an active site which is where the catalytic activity occurs
• the active site is a part of the 3D tertiary protein structure of an enzyme that is responsible for its catalytic activity
• a biological reactant, known as a substrate, attaches to the active site so that a chemical reaction can happen

Question 14

describe the lock and key theory

Answer 14

• the lock and key theory = the substrate must fit exactly in the active site, with the correct orientation, in order for a reaction to happen
• the substrate must also temp bond to the active site through intermolecular forces. this decrease the activation energy needed for the reaction t occur by promoting the movement of electrons
• only the correctly shaped substrate can fit into the active site of the enzyme. This means that eve the wrong stereoisomer (enantiomer) will not be catalyse by the enzyme. an enzyme is therefore stereospecific
• we see stereospecificity in enzymes because they’re made up of amino acids which themselves contain chiral centres

Question 15

why do we use modelling enzymes and how do we use them?

Answer 15

• finding new drugs is time consuming> computers use to visualise an enzyme’s active site
• scientists can very quickly predict which drugs will it into the active site before they decide to synthesise them
• this helps to design drugs that can b used to treat a range of medical conditions

Question 16

describe the structure of DNA

Answer 16

• DNA is a condensation polymer made of 4 monomers known as nucleotides
• the condensation reaction is between the phosphate group of nucleotide and between the phosphate group of one nucleotide and the pentose sugar group of another -> this creates a sugar- phosphate backbone that acts as the spine of the DNA strand
• water is produced in this reaction and further links can be made as there are still Oh groups available to form new sugar- phosphate bonds

Question 17

How does Cisplatin work and what is it used for?

Answer 17

• Cisplatin is a complex containing platinum (II) and is one of the most effective drugs used for fighting cancer
• cancer is caused by the body losing control of the replication of cells. Cells need to divide and to do this they replicate their DNA
• Cisplatin binds to the DNA, preventing its replication. This leads to the cell being destroyed.
• cisplatin prevents replication by distorting the shape of the DNA
• the platinum ion in cisplatin substitutes its chorine ligands to from 2 co-ordinate bonds with nitrogen atoms on 2 adjacent guanine bases.
• the NDA strands are then kinked, so they cannot unravel properly to replicate

Question 18

what are the disadvantages of Cisplatin?

Answer 18

• it has some nasty side effects because it binds to healthy cells as well as the cancer cells
• this causes hair loss, fatigue and sickness in patients.
• the hair loss happens because Cisplatin attacks cells that divide quickly, such as harr follicles