amino acids, proteins and DNA

Question 1

structure of amino acid

Answer 1

H
H2N-C-COOH
R

• chiral C
• 20 naturally occurring

Question 2

because they have the f groups … they have both …. properties

Answer 2

because they have the f groups of amine (base) and carboxylic acid, they have both basic and acidic properties

Question 3

at low pH what happens to amino acid

Answer 3

low pH so high acidity

so amine will be protonated. because high [H+] so more likely to act as proton acceptor
NH2 —> NH3+

already high [H+] so acid less likely to deprotonate. links to le chatelier; the deprotonation is energetically unfavourable

!!! also side groups

Question 4

at high pH what happens to structure of amino acid

Answer 4

c acid is deprotonated
COOH –> COO-

low [H+] and high [OH-] so H+ is donated to base, OH-, forming water

!!! also side groups

Question 5

at neutral pH 7, what happens to amino acid structure

Answer 5

zwitter ion structure - name for when formal charge separation but overall electrically neutral molecule. so if side groups also give charges, not zwitterion

acid is deprotonated and amine group is protonated

!!! also side groups

Question 6

about the zwitter ion

Answer 6

• has a formal charge separation
• H+ from c.acid protonates amine
• overall neutral molecule

Question 7

why can amino acids and thus proteins (have nh2 and cooh group on either end) act as buffers

Answer 7

the no charge form of amino acid never occurs because COOH acts as acid and NH3 acts as base

so they are weak buffers because if H+ OR OH- is added:

+NH3[]COO- + HCl –> Cl- NH3+[]COOH
- the chloride ion forms ionic bond with the nh3+ and the h+ protonated the carboxylate ion (conjugate base)

+NH3[]COO- + NaOH —> NH2[]COO-Na+ +H2O
- the Na+ forms ionic bond withcarboxylate ion and nh3 releases a proton (conjugate acid)

the [] in the middle is the bit of the amino acid unimportant

Question 8

what are the IMFs and state of amino acids

Answer 8

• there are strong ionic attractions between z. ions
• so very high IMFs
• so solid

other molecules of similar Mr would be liquid

Question 9

naming amino acids

Answer 9

will always have suffix of oic acid (unless main chain has 2 c acids, then dioic acid) because priority

count longest chain length

which C is amine group on relative to C1, the one in the c acid f group

don’t forget side groups and any f groups in R group

Question 10

what is there to say about the optical isomerism of amino acids

Answer 10

chiral C in all but one amino acid (glycine because r group is a H)
so could exist as two enantiomers
however in nature only one enantiomer is presented

!! the left handed thing that silly ps was saying!

Question 11

what reactions can amino acids undergo

Answer 11

HAS AN AMINE GROUP SO CAN
- be protonated (acid base)
- react with acyl chlorides or acid anhydrides to form n sub (2ndary) amides . nucleophilic addition elimination
- n sub with h alkanes. amines are nucleophiles

HAS A C ACID GROUP SO CAN
- be deprotonated (acid base)
- esterification with alcohols

Question 12

dipeptide

polypeptide

Answer 12

two amino acids joined together in a condensation reaction to form one molecule. c acid OH and H from NH2 are removed, which forms the water (small molecule) released.

several amino acids joined together into a condensation polymer (which is the polypeptide). water as other product. for n monomers, 2n-1 waters formed (?)

Question 13

how are peptides formed and how can they be broken down

Answer 13

condensation reactions of amino acids

reacting with water, hydrolysis. conditions 4M HCl and cook. acts as catalyst. forms the amino acids that was forming the dipeptide. they aren’t in no charge form, never are; they will be nh3+ because conc HCl (acidic, low pH)

Question 14

when two amino acids join together to form a dipeptide

Answer 14

unless its the same amino acid, there are two different options of dipeptides could form. because depends on, say for amino acid 1, whether its NH2 group or COO group reacts.

shortcut for it: switch r groups

Question 15

why can amino acids react with acyl chlorides or acid anhydrides?

which part?

Answer 15

because amine (n in the amine group) is a nucleophile so attracted to delta +ve charge on C.

not the OH in COOH, because although they do react with alcohols (lone pair on O; is a nucleophile) the COOH dissociates int COO- and then the negative charge is delocalised, making it more stable (like a benzene ring). so won’t do mechanism, because won’t disrupt delocalisation by doing addition

Question 16

bio = peptide bond ;

in chem =

Answer 16

amide functional group

CONH

Question 17

about proteins

Answer 17

• sequences of amino acids joined by peptide links
• condensation polymers of amino acids
• naturally occurring polymers
• large complicated molecules, described by their structure

Question 18

primary structure

Answer 18

sequence of amino acids which are held together by covalent amide bonds

Question 19

secondary structure

Answer 19

h bonding within an amino acid sequence (polypeptide) makes it non linear

there is coiling into alpha helices and beta pleated sheets
- a: more common. 3d arrangement
- b: when there are antiparallel sections and h bonding between them
- the N-H on one and the C=O on another. the delta +ve H and the delta -ve O

Question 20

tertiary structure

what is SS bridge

Answer 20

3D shape due to coiling and folding. H bonding, ionic interactions and S-S bridges between R groups (rather than the atoms in CONH for 2ndary)

disulphide bridges form when the SH (thiol) R group in cysteine get close enough. the Ss are oxidised, losing e- and H+
S-S bridges stabilise structure

Question 21

what can the structures be affected by

Answer 21

temp or pH. these affect h bonding, ionic bonding and the formation of disulphide bridges

wider: S-S bridges only formed in ER not cytoplasm because needs oxidative envt and cytoplasm is reductive. so no ss bridges formed in cytoplasm, thiol groups remain in reduced form. good for keeping protein structure

Question 22

enzymes [6]

Answer 22

• proteins
• biological catalysts; can increase rate by a million or even billion trillion times ?!
• have an active site wherein the Ea is much much lower. active site attracts substrate to it
• can be inhibited by drugs
• forms e-s complex then e-product complex then product is released
• stereospecific

Question 23

what does it mean that enzymes are stereospecific (have stereospecific active sites)

Answer 23

they are made of amino acids and therefore have chiral centres. which makes their active sites stereospecific, they only work with one enantiomer of substrate

recall that enantiomers have the same chemical properties except with plane polarised light and with other enantiomeric molecules

Question 24

active site

Answer 24

hollow in the globular structure

substrate binds with side chains through various interactions: VdW, H bonding, D-D, ionic interactions

interaction needs to be strong enough that substrate is held for long enough so enzyme-catalysed reaction occurs, but weak enough for product to be released

Question 25

CADD

Answer 25

computer aided drug discovery computers can be used to design drugs that act as enzyme inhibitors. antibiotics eg prevent enzyme involved in cell wall (murein) formation so bacteria lyse computers can help in drug devt by modelling the shape of an active site to predict drug efficacy. it allows scientists to look for drugs that might have correct shape before they start to make and test (HTST?)

Question 25

drugs as enzyme inhibitors - what are inhibitors what determines how much inhibition takes place?

Answer 25

molecule that binds to the active site/allosteric site of an enzyme, preventing it form performing its function. blocks its activity - similar enough shape that binds to enzyme - but doesnt react obvs - so doesnt dissociate (?) from active sie. so active site remains occupied - the relative [ ] of substrate and inhibitor determines how much inhibition takes place (comp. inhibitor) - the strength of the bonding between inhibitor and active site of enzyme determines how much inhibition takes place. therefore inhibitor must bind more strongly than substrate

Question 25

why can a stereospecific active site only bond to one enantiomeric form of a substrate or drug?

Answer 25

made of chiral amino acids, which inherently makes the active sites chiral. they inherently prefer one stereoisomer over the other enantiomers are mirror images of each other, so while one fits into the active site, the other may not align properly with the binding pockets or catalytic residues. binding relies on interactions eg hydrogen bonding, ionic interactions, hydrophobic effects, and VdW. these are highly spatially specific, so only one enantiomer will have the right orientation to form the correct interactions.

Question 25

about DNA [4]

Answer 25

- double helix - 2 complementary polynucleotide chains/strands (polymers) joined together by H bonding between nitrogenous bases in nucleotides (monomers) - chains are antiparallel, running in opposite directions - sugar phosphate sugar phosphate polymer chain as backbone

Question 25

where else have we come across the idea of interactions needing to be not too strong not too weak

Answer 25

active sites in solid heterogenous catalysts (TMs) - site in catalyst where adsorption can occur - adsorption needs to be strong enough so reactants adsorb, so local conc is increased on surface catalyst and bonds weakened - weak enough that they can ad/desorb over and over so moving across catalyst, so frequency of *successful* collisions increased - weak enough so products desorb

Question 26

structure and bonding of a nucleotide

Answer 26

phosphate, 2-deoxyribose, one of four nitrogenous bases condensation reactions join them together to form one nucleotide condensation reaction between OH on phosphate and H from the OH on the sugar forms (phosphodiester covalent bonds which make up) the sugar phosphate backbone of the double helix known in chem as the sugar phosphate-sugar-phosphate polymer chain with bases attached to the sugars in the chain.

Question 27

how is a nucleotide formed

Answer 27

the OH in phosphate reacts with H on the top OH of the deoxyribose water lost there, there's bond between them like P-O-CH2 etc the other top OH of deoxyribose reacts with a H from NH of the bases water lost there, there's bond between them like C (in skeletal structure of ribose) - N - rest of base

Question 28

A single strand of DNA is a [] linked by [] between the [] of one nucleotide and the [] of another nucleotide. This results in a [] with bases attached to the sugars in the chain.

Answer 28

A single strand of DNA (deoxyribonucleic acid) is a *polymer of nucleotides* linked by *covalent* bonds between the *phosphate group* of one nucleotide and the *2-deoxyribose* of another nucleotide. This results in a *sugar phosphate-sugar-phosphate polymer chain* with bases attached to the sugars in the chain.

Question 29

how does hydrogen bonding between base pairs lead to the two complementary strands of DNA.

Answer 29

Complementary means the two strands must have base sequences that match all A to T and C to G Hydrogen bonding between base pairs leads to the two complementary strands of DNA. 3 hydrogen bonds between G and C 2 between A and T look at picture

Question 30

what is cisplatin shape and structure

Answer 30

- cancer drug - TM ion complex - Pt (II) is central metal atom - arranged in square planar format with 2 NH3 groups and 2 Cl- groups. because there are two of one type of ligand, and its a square planar shape, the complex exhibits geometric isomerism. only the Z isomer works as anticancer drug, where the Cl-s are on one side of Pt (not opposite each other) and NH3s are on one side.

Question 31

how does cisplatin work why does this mean only its Z isomer works as a drug

Answer 31

Cisplatin prevents DNA replication in cancer cells it does this via a ligand replacement reaction with DNA: a bond is formed between platinum and a nitrogen atom on guanine. both Cl- ions are lost from the Pt, which is why they must both be on the same side. once the Cl-s are displaced, Pt can join onto DNA by coordinate bond (N on guanine gives LP to Pt, it acts as lewis base)

Question 32

society needs to assess the balance between [] of drugs such as the anticancer drug cisplatin. why

Answer 32

society needs to assess the balance between *the benefits and adverse effects* of drugs such as the anticancer drug cisplatin. cisplatin causes adverse side effects such as hair loss because it is not selective, and prevents DNA replication of healthy somatic cells as well. Unwanted side effects can be minimised by giving cis-platin in small doses.

Question 33

how can amino acids be separated and identified

Answer 33

thin layer chromatography stationary phase: solid Al2O3 or SiO2 mobile phase: organic solvent Rf values show how soluble they are (high affinity for solvent) or insoluble (high retention in s phase). a high Rf value means higher solubility. Rf values are the same if same conditions therfore can be identified by it

Question 34

the chromatogram can be developed how

Answer 34

in order to "see" the amino acids because they are invisible to naked eye, they can be developed with: **ninhydrin,** which used to detect ammonia and amines. upon reaction with these amines, ninhydrin gets converted into deep blue or purple or **uv light** can be shone which interacts with some fluorescent material in the chromatography paper, so the amino acids points stay dark/normal. so identified. pencil shape around it