organics - amino acids, proteins and DNA

Question 1

what are the functional groups of an amino acid

Answer 1

-amine - NH2
-carboxylic acid - COOH

Question 1

how are amino acids amphoteric

Answer 1

• amine gives basic character and carboxylic acid gives acidic character

Question 2

what part of the amino acid molecule varies

Answer 2

the R group

Question 3

how are most amino acids chiral

Answer 3

• 4 functional groups surrounding C
  -COOH, NH2,H and R

Question 4

what does each amino acid exist as

Answer 4

a zwitterion - as each amine group is protonated by a carboxylic acid group on another molecule

Question 5

what is a zwitterion

Answer 5

-species that has both a +ve and -ve charge on different parts of the particle
-this means that amino acids are solid at room temp as there is ionic attraction between the zwitterions

Question 6

what 3 types of molecule can the R group of an amino acid be

Answer 6

-acidic - has COOH
-basic - has OH
-neutral - has neither

Question 7

what happens to an amino acid if the pH is lowered

Answer 7

-the COO- part of zwitterion will accept a H+ ion to reform COOH
-causes NH2 to become +NH3

Question 8

what happens if the pH is raised/ base added

Answer 8

-+NH3 part of the zwitterion will donate a H+ to reform the NH2 group
-causes COOH to become COO-
also need to add ion onto R group if it contains COOH

Question 9

what reactions can the amine part of an amino acid undergo

Answer 9

-protonated by acids
-acylation with acyl chloride/ acid anhydride -nucleophilic sub with halogenoalkanes

Question 10

what reactions can the carboxylic acid part of an amino acid undergo

Answer 10

-deprotonated by bases
-esterification with alcohols and conc H2SO4

Question 11

how are peptides formed from amino acids

Answer 11

-in a condensation reaction - join to make dipeptides or polypeptides
-lose molecule of water
-take OH of COOH and H of NH2

Question 12

how can proteins and peptides be broken down

Answer 12

-by hydrolysis
-uses water to make to constituent amino acids

Question 13

what is a polypeptide

Answer 13

-long chain molecule formed from many amino acid monomers
-joined together by covalent bonds linking the chains

Question 14

what is the primary structure of a protein

Answer 14

-sequence of amino acids bonded by covalent peptide bonds
-primary structure is specific to each protein - one alteration can affect the functioning of the protein

Question 15

what is the secondary structure of a protien

Answer 15

-occurs when the weak -ve N and O interact with the +ve H and form hydrogen bonds - amino and carboxyl group
-two shapes - a helix and beta pleated sheet
-can be broken at high temp and pH changes as distort the structure

Question 16

how does the a helix shape occur in a protein

Answer 16

-H bonds form bwt every 4th peptide bond
-bwt the oxygen of the COOH and the H of NH2

Question 17

how does the beta pleated sheet shape occur

Answer 17

-where the protein folds so that two parts of the polypeptide chain are parallel to each other
-enable H bonds to form bwt the parallel bonds

Question 18

what is the tertiary structure of a polypeptide

Answer 18

-3D arrangement of a single polypeptide chain
- additional bonds form bwt the R groups
-these are
-hydrogen - only bwt R group
-disulphide - only bwt cysteine AA
-ionic - occurs bwt charged R groups
-van der waals - bwt non-polar R groups

Question 19

what is the quaternary structure of a protein

Answer 19

-arrangement of multiple polypeptide chains or subunits in a protein complex

Question 20

how are proteins hydrolysed

Answer 20

-polypeptides broken down into amino acids by adding water
-reflux
-conc hydrochloric acid
-boiled as the reaction is slow
-if add enzyme then reaction occurs at room temp

Question 21

what method is used to identify an amino acids

Answer 21

-after hydrolysis is done use Thin Layer Chromotography

Question 22

how does thin layer chromatography work

Answer 22

Step 1:

Prepare a beaker with a small quantity of solvent

Step 2:

On a TLC plate, draw a horizontal line at the bottom edge (in pencil)

This is called the baseline

Step 3:

Place a spot of pure reference compound on the left of this line, then a spot of the sample to be analysed to the right of the baseline and allow to air dry

The reference compounds will allow identification of the mixture of compounds in the sample

Step 4:

Place the TLC plate inside the beaker with solvent - making sure that the solvent does not cover the spot - and place a lid to cover the beaker

The solvent will begin to travel up the plate, dissolving the compounds as it does

Step 5:

As solvent reaches the top, remove the plate and draw another pencil line where the solvent has reached, indicating the solvent front

The sample’s components will have separated and travelled up towards this solvent front

step 6:
calculate the Rf value
by
distance moved by component/ distance moved by solvent

Question 23

what are the two phases of TLC

Answer 23

-stationary
-mobile

Question 24

what is the stationary phase of TLC

Answer 24

-the phase is commonly a thin plastic/metal sheet coated in silica (or alumia) -the solute molecules adsorb onto the surface -depending on the strength of interactions with the stationary phase the separated components will travel particular distances through the plate -the more they interact with the stationary phase the more they will stick to it

Question 25

what is the mobile phase

Answer 25

-flows over the stationary phase -it is a polar or non-polar solvent that carries the components of the compound being investigated -polar solvents = water or alcohol -non-polar = alkanes

Question 26

how are the components identified in TLC

Answer 26

-if the components are coloured the spots are easily identified on the chromatogram -if the components are not coloured then we can locate the spots and draw around them in pencil -this is done by -UV light -ninhydrin - carcinogenic -potassium manganate -iodine vapour

Question 27

why should the baseline/ start line be drawn on in pencil

Answer 27

-any other medium would interact with the ample components and solvent -so would contaminate it

Question 28

why do the amino acids separate in TLC

Answer 28

-depends on each AA affinity for the stationary phase compared to the affinity for the mobile phase -depends on the IMF acting bwt the AA and solvent -stronger they are the closer they are to the solvent front

Question 29

why is a lid placed over the tank of the amino acid TLC

Answer 29

-so that the inside of the tank is saturated with solvent vapour and the solvent can then travel up the plate

Question 30

what are enzymes

Answer 30

biological catalysts -speed up the rate of reactions without being used up or changed

Question 31

what is the site of binding known as in an enzymes and why is it specific

Answer 31

Enzymes have an active site where specific substrates bind forming an enzyme-substrate complex The active site of an enzyme has a specific shape to fit a specific substrate- due to the bonds that hold the tertiary structure Extremes of heat or pH can change the shape of the active site, preventing substrate binding – this is called denaturation Substrates collide with the enzymes active site and this must happen at the correct orientation and speed in order for a reaction to occur

Question 32

what enables an enzyme to be specific

Answer 32

The specificity of an enzyme is a result of the complementary nature between the shape of the active site on the enzyme and its substrate(s) The shape of the active site (and therefore the specificity of the enzyme) is determined by the complex tertiary structure of the protein that makes up the enzyme: Proteins are formed from chains of amino acids held together by peptide bonds The order of amino acids determines the shape of an enzyme If the order is altered, the resulting three-dimensional shape changes

Question 33

how do drugs inhibit enzymes

Answer 33

Most drugs work by their ability to bind to receptors stopping their normal biological activity and interrupting the development of disease Drugs bind to receptors generally using intermolecular forces or ionic bonds The stronger the interaction the more effective the drug activity

Question 34

how does optical isomerism in drugs affect enzymes

Answer 34

Many naturally occurring organic molecules consist of enantiomers, in which only one enantiomer is biologically active Similarly, many drugs have enantiomeric forms in which only one form of the drug is active The site where the drug binds to the biomolecule can only accept one orientation; it is said to be stereoselective

Question 35

what is DNA

Answer 35

deoxyribonucleic acid -two stranded double helix molecule - 3D -polynucleotide - many nucleotides bonded together in a long chain

Question 36

what is DNA made up of

Answer 36

-phosphate group - it is an ion -2-deoxyribose - 4 base pairs -adenine -thymine -guanine -cytosine

Question 37

what is a nucleotide made up of

Answer 37

-phosphate -sugar -base

Question 38

what holds the sugar-phosphate backbone together

Answer 38

-covalent bonds known as phosphodiester bonds

Question 39

what are the bonds bwt base pairs and how do u find them on the individual molecule

Answer 39

-hydrogen bonds -look for single NH

Question 40

what way does the sugar phosphate backbones on the two strands run

Answer 40

-antiparallel -one way 3'-5' -the other -5' to 3'

Question 41

what are the comp base pairs

Answer 41

-adenine and thymine -guanine and cytosine

Question 42

what enables DNA to break apart in transcription

Answer 42

-weak hydrogen bonds are more easily broken than the covalent bonds in the sugar-phosphate backbone -enable exposed bases to occur

Question 43

what is the structure and shape of cisplatin

Answer 43

square planar Cl I NH3- Pt - Cl I NH3 Pt is central molecule

Question 44

what is cisplatin

Answer 44

anti-cancer drug

Question 45

how does cisplatin work

Answer 45

-The cis-platin passes through the cell membrane and undergoes ligand exchange where the chlorines are replaced by water molecules -The nitrogen on a guanine base is a better ligand than water and forms dative covalent bonds with the cis-platin -the lone pair of electrons on the nitrogen form a dative covalent bond with the platinum -the other chlorine then does the same -The cis-platin distorts the shape of the DNA and prevents the DNA from replicating - kinks the strand

Question 46

what are the benefits of cisplatin as an anti cancer drug

Answer 46

-greater effect on cancer cells as it bonds to the DNA as cancer cells replicate faster than healthy cells -so treats cancer

Question 47

what are the adverse affects of cisplatin

Answer 47

- other healthy cells which replicate quickly, such as hair follicles, are also affected by cis-platin -This is why hair loss is a side-effect of people undergoing cancer treatment -New therapeutic pathways are constantly under development that aim to deliver drugs that target cancer cells while leaving healthy cells untouched -supression of immune system -kidney damage

Question 48

which nitrogen bonds to the platinum

Answer 48

the 7th one -which is adjacent/across the valley from the C=O